scholarly journals Ancestral gene synteny reconstruction improves extant species scaffolding

2015 ◽  
Author(s):  
Yoann Anselmetti ◽  
Vincent Berry ◽  
Cedric Chauve ◽  
Annie Chateau ◽  
Eric Tannier ◽  
...  
Keyword(s):  
Solution Space ◽  
Ancestral Genome ◽  
Ensembl Database ◽  
Data Set ◽  
Ancestral Gene ◽  
Ancestral Genome Reconstruction ◽  
Extant Species ◽  
Reduced Data ◽  
Very High

We exploit the methodological similarity between ancestral genome reconstruction and extant genome scaffolding. We present a method, called \decopp\ that constructs neighborhood relationships between genes or contigs, in both ancestral and extant genomes, in a phylogenetic context. It is able to handle dozens of complete genomes, including genes with complex histories, by using gene phylogenies reconciled with a species tree, that is, annotated with speciation, duplication and loss events. Reconstructed ancestral or extant synteny comes with a support computed from an exhaustive exploration of the solution space. We compare our method with a previously published one that follows the same goal on a small number of genomes with universal unicopy genes. Then we test it on the whole Ensembl database, by proposing partial ancestral genome structures, as well as a more complete scaffolding for many partially assembled genomes on 69 eukaryote species. We carefully analyze a couple of extant adjacencies proposed by our method, and show that they are indeed real links in the extant genomes, that were missing in the current assembly. On a reduced data set of 39 eutherian mammals, we estimate the precision and sensitivity of \decopp\ by simulating a fragmentation in some well assembled genomes, and measure how many adjacencies are recovered. We find a very high precision, while the sensitivity depends on the quality of the data and on the proximity of closely related genomes.

scholarly journals A Frequency-Based Approach for the Detection and Classification of Structural Changes Using t-SNE †

Sensors ◽  
2019 ◽  
Vol 19 (23) ◽  
pp. 5097 ◽  
Author(s):  
David Agis ◽  
Francesc Pozo
Keyword(s):  
Structural Changes ◽  
Dimensional Space ◽  
Principal Component ◽  
Majority Voting ◽  
Data Set ◽  
Centroid Distance ◽  
Low Dimensional ◽  
Reduced Data

This work presents a structural health monitoring (SHM) approach for the detection and classification of structural changes. The proposed strategy is based on t-distributed stochastic neighbor embedding (t-SNE), a nonlinear procedure that is able to represent the local structure of high-dimensional data in a low-dimensional space. The steps of the detection and classification procedure are: (i) the data collected are scaled using mean-centered group scaling (MCGS); (ii) then principal component analysis (PCA) is applied to reduce the dimensionality of the data set; (iii) t-SNE is applied to represent the scaled and reduced data as points in a plane defining as many clusters as different structural states; and (iv) the current structure to be diagnosed will be associated with a cluster or structural state based on three strategies: (a) the smallest point-centroid distance; (b) majority voting; and (c) the sum of the inverse distances. The combination of PCA and t-SNE improves the quality of the clusters related to the structural states. The method is evaluated using experimental data from an aluminum plate with four piezoelectric transducers (PZTs). Results are illustrated in frequency domain, and they manifest the high classification accuracy and the strong performance of this method.

A unified ILP framework for core ancestral genome reconstruction problems

2020 ◽  
Vol 36 (10) ◽  
pp. 2993-3003 ◽  
Author(s):  
Pavel Avdeyev ◽  
Nikita Alexeev ◽  
Yongwu Rong ◽  
Max A Alekseyev
Keyword(s):  
Genome Rearrangements ◽  
Supplementary Information ◽  
Whole Genome ◽  
Ancestral Genome ◽  
Genome Reconstruction ◽  
Polynomial Size ◽  
Extensive Evaluation ◽  
Ancestral Genome Reconstruction ◽  
Extant Species ◽  
Genome Duplications

Abstract Motivation One of the key computational problems in comparative genomics is the reconstruction of genomes of ancestral species based on genomes of extant species. Since most dramatic changes in genomic architectures are caused by genome rearrangements, this problem is often posed as minimization of the number of genome rearrangements between extant and ancestral genomes. The basic case of three given genomes is known as the genome median problem. Whole-genome duplications (WGDs) represent yet another type of dramatic evolutionary events and inspire the reconstruction of preduplicated ancestral genomes, referred to as the genome halving problem. Generalization of WGDs to whole-genome multiplication events leads to the genome aliquoting problem. Results In this study, we propose polynomial-size integer linear programming (ILP) formulations for the aforementioned problems. We further obtain such formulations for the restricted and conserved versions of the median and halving problems, which have been recently introduced to improve biological relevance of the solutions. Extensive evaluation of solutions to the different ILP problems demonstrates their good accuracy. Furthermore, since the ILP formulations for the conserved versions have linear size, they provide a novel practical approach to ancestral genome reconstruction, which combines the advantages of homology- and rearrangements-based methods. Availability and implementation Code and data are available in https://github.com/AvdeevPavel/ILP-WGD-reconstructor. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Inversion of seismic refraction data using genetic algorithms

Geophysics ◽  
1996 ◽  
Vol 61 (6) ◽  
pp. 1715-1727 ◽  
Author(s):  
Fabio Boschetti ◽  
Mike C. Dentith ◽  
Ron D. List
Keyword(s):  
Genetic Algorithm ◽  
Genetic Algorithms ◽  
Seismic Refraction ◽  
Solution Space ◽  
Optimization Methods ◽  
Data Set ◽  
Weathered Layer ◽  
Seismic Refraction Data ◽  
Refraction Data

The use of genetic algorithms in geophysical inverse problems is a relatively recent development and offers many advantages in dealing with the nonlinearity inherent in such applications. However, in their application to specific problems, as with all algorithms, problems of implementation arise. After extensive numerical tests, we implemented a genetic algorithm to efficiently invert several sets of synthetic seismic refraction data. In particular, we aimed at overcoming one of the main problems in the application of genetic algorithms to geophysical problems: i.e., high dimensionality. The addition of a pseudo‐subspace method to the genetic algorithm, whereby the complexity and dimensionality of a problem is progressively increased during the inversion, improves the convergence of the process. The method allows the region of the solution space containing the global minimum to be quickly found. The use of local optimization methods at the last stage of the search further improves the quality of the inversion. The genetic algorithm has been tested on a field data set to determine the structure and base of the weathered layer (regolith) overlaying a basement of granite and greenstones in an Archaean terrain of Western Australia.

Ground water quality of selected areas of Punjab and Sind Provinces, Pakistan: Chemical and microbiological aspects

2019 ◽  
Author(s):  
Chem Int
Keyword(s):  
Ionic Concentration ◽  
Chloride Ions ◽  
Potassium Ions ◽  
Ammonium Ions ◽  
High Concentration ◽  
Phosphate Ions ◽  
Sodium Magnesium ◽  
Very High ◽  
Microbiological Aspects

The assessment of groundwater is essential for the estimation of suitability of water for safe use. An attempt has been made to study the groundwater of selected areas of Punjab (Sheikhupura & Sahiwal) and Sindh (Sindh, Jawar Dharki and Dharki), Pakistan. The results indicate that pH, color and odor were all within limits of WHO that is pH ranges 6.5–8.5, colorless and odorless, respectively. The high values of suspended solids were observed in the Sindh-1 and Dharki samples. Microbiologically only Sahiwal and Jawar Dharki were found fit for drinking purpose. Trace metals analysis of Sheikhupura-1 and Sindh-1 showed that values do not fall within limits of WHO for Iron. The ionic concentration analysis showed that high bicarbonate (HCO3-), ions are present in the samples of Sahiwal and Dharki; Sindh-1 and Jawar Dharki samples showed very high concentration for chloride ions, all samples were satisfactory level for sulphate (SO42-), sodium, magnesium and phosphate ions except samples of Sindh-1 and Jawar Dharki. High concentration of calcium and potassium ions was observed in samples of Sindh-1, while all other samples were found fit for drinking purposes in respect of nitrate, nitrite and ammonium ions. The high concentration of Fluoride was found only in Sheikhupura-2 samples.

Quality-of-Life Measurement in Advanced Cancer: Assessing the Individual

1999 ◽  
Vol 17 (11) ◽  
pp. 3603-3611 ◽  
Author(s):  
Dympna Waldron ◽  
Ciaran A. O'Boyle ◽  
Michael Kearney ◽  
Michael Moriarty ◽  
Desmond Carney
Keyword(s):  
Quality Of Life ◽  
Advanced Cancer ◽  
Internal Validity ◽  
Semistructured Interview ◽  
Incurable Cancer ◽  
Life Measurement ◽  
The Difference ◽  
The Individual ◽  
Very High

PURPOSE: Despite the increasing importance of assessing quality of life (QoL) in patients with advanced cancer, relatively little is known about individual patient's perceptions of the issues contributing to their QoL. The Schedule for the Evaluation of Individual Quality of Life (SEIQoL) and the shorter SEIQoL–Direct Weighting (SEIQoL-DW) assess individualized QoL using a semistructured interview technique. Here we report findings from the first administration of the SEIQoL and SEIQoL-DW to patients with advanced incurable cancer. PATIENTS AND METHODS: QoL was assessed on a single occasion using the SEIQoL and SEIQoL-DW in 80 patients with advanced incurable cancer. RESULTS: All patients were able to complete the SEIQoL-DW, and 78% completed the SEIQoL. Of a possible score of 100, the median QoL global score was as follows: SEIQoL, 61 (range, 24 to 94); SEIQoL-DW, 60.5 (range, 6 to 95). Psychometric data for SEIQoL indicated very high levels of internal consistency (median r = .90) and internal validity (median R2 = 0.88). Patients' judgments of their QoL were unique to the individual. Family concerns were almost universally rated as more important than health, the difference being significant when measured using the SEIQoL-DW (P = .002). CONCLUSION: Patients with advanced incurable cancer were very good judges of their QoL, and many patients rated their QoL as good. Judgments were highly individual, with very high levels of consistency and validity. The primacy given to health in many QoL questionnaires may be questioned in this population. The implications of these findings are discussed with regard to clinical assessment and advance directives.

scholarly journals Calling for improved quality in the registration of traditional Chinese medicine during the public health emergency: a survey of trial registries for COVID-19, H1N1, and SARS

Trials ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Zhuoran Kuang ◽  
◽  
Xiaoyan Li ◽  
Jianxiong Cai ◽  
Yaolong Chen ◽  
...  
Keyword(s):  
Clinical Trial ◽  
Clinical Trials ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Secondary Outcome ◽  
Specific Information ◽  
Clinical Trial Registry ◽  
Data Set ◽  
Diagnosis Criteria

Abstract Objective To assess the registration quality of traditional Chinese medicine (TCM) clinical trials for COVID-19, H1N1, and SARS. Method We searched for clinical trial registrations of TCM in the WHO International Clinical Trials Registry Platform (ICTRP) and Chinese Clinical Trial Registry (ChiCTR) on April 30, 2020. The registration quality assessment is based on the WHO Trial Registration Data Set (Version 1.3.1) and extra items for TCM information, including TCM background, theoretical origin, specific diagnosis criteria, description of intervention, and outcomes. Results A total of 136 records were examined, including 129 severe acute respiratory syndrome coronavirus 2 (COVID-19) and 7 H1N1 influenza (H1N1) patients. The deficiencies in the registration of TCM clinical trials (CTs) mainly focus on a low percentage reporting detailed information about interventions (46.6%), primary outcome(s) (37.7%), and key secondary outcome(s) (18.4%) and a lack of summary result (0%). For the TCM items, none of the clinical trial registrations reported the TCM background and rationale; only 6.6% provided the TCM diagnosis criteria or a description of the TCM intervention; and 27.9% provided TCM outcome(s). Conclusion Overall, although the number of registrations of TCM CTs increased, the registration quality was low. The registration quality of TCM CTs should be improved by more detailed reporting of interventions and outcomes, TCM-specific information, and sharing of the result data.

scholarly journals Galileo L10 Satellites: Orbit, Clock and Signal-in-Space Performance Analysis

Sensors ◽  
2021 ◽  
Vol 21 (5) ◽  
pp. 1695
Author(s):  
Constantin-Octavian Andrei ◽  
Sonja Lahtinen ◽  
Markku Poutanen ◽  
Hannu Koivula ◽  
Jan Johansson
Keyword(s):  
Performance Indicators ◽  
Satellite System ◽  
Short Term ◽  
Orbital Inclination ◽  
Navigation Data ◽  
Periodic Signals ◽  
Global Navigation Satellite ◽  
Minor Correction ◽  
Very High

The tenth launch (L10) of the European Global Navigation Satellite System Galileo filled in all orbital slots in the constellation. The launch carried four Galileo satellites and took place in July 2018. The satellites were declared operational in February 2019. In this study, we report on the performance of the Galileo L10 satellites in terms of orbital inclination and repeat period parameters, broadcast satellite clocks and signal in space (SiS) performance indicators. We used all available broadcast navigation data from the IGS consolidated navigation files. These satellites have not been reported in the previous studies. First, the orbital inclination (56.7±0.15°) and repeat period (50680.7±0.22 s) for all four satellites are within the nominal values. The data analysis reveals also 13.5-, 27-, 177- and 354-days periodic signals. Second, the broadcast satellite clocks show different correction magnitude due to different trends in the bias component. One clock switch and several other minor correction jumps have occurred since the satellites were declared operational. Short-term discontinuities are within ±1 ps/s, whereas clock accuracy values are constantly below 0.20 m (root-mean-square—rms). Finally, the SiS performance has been very high in terms of availability and accuracy. Monthly SiS availability has been constantly above the target value of 87% and much higher in 2020 as compared to 2019. Monthly SiS accuracy has been below 0.20 m (95th percentile) and below 0.40 m (99th percentile). The performance figures depend on the content and quality of the consolidated navigation files as well as the precise reference products. Nevertheless, these levels of accuracy are well below the 7 m threshold (95th percentile) specified in the Galileo service definition document.

Simple Index to Assess the Calibration Quality of Safety Performance Functions Based on Multiple Goodness-of-Fit Metrics

2021 ◽  
pp. 036119812110088
Author(s):  
Raul E. Avelar ◽  
Karen Dixon ◽  
Boniphace Kutela ◽  
Sam Klump ◽  
Beth Wemple ◽  
...  
Keyword(s):  
Goodness Of Fit ◽  
Synthetic Data ◽  
Calibration Procedure ◽  
Safety Performance ◽  
Absolute Deviation ◽  
Data Set ◽  
Safety Database ◽  
Simple Index ◽  
Safety Performance Functions

The calibration of safety performance functions (SPFs) is a mechanism included in the Highway Safety Manual (HSM) to adjust SPFs in the HSM for use in intended jurisdictions. Critically, the quality of the calibration procedure must be assessed before using the calibrated SPFs. Multiple resources to aid practitioners in calibrating SPFs have been developed in the years following the publication of the HSM 1st edition. Similarly, the literature suggests multiple ways to assess the goodness-of-fit (GOF) of a calibrated SPF to a data set from a given jurisdiction. This paper uses the calibration results of multiple intersection SPFs to a large Mississippi safety database to examine the relations between multiple GOF metrics. The goal is to develop a sensible single index that leverages the joint information from multiple GOF metrics to assess overall quality of calibration. A factor analysis applied to the calibration results revealed three underlying factors explaining 76% of the variability in the data. From these results, the authors developed an index and performed a sensitivity analysis. The key metrics were found to be, in descending order: the deviation of the cumulative residual (CURE) plot from the 95% confidence area, the mean absolute deviation, the modified R-squared, and the value of the calibration factor. This paper also presents comparisons between the index and alternative scoring strategies, as well as an effort to verify the results using synthetic data. The developed index is recommended to comprehensively assess the quality of the calibrated intersection SPFs.

scholarly journals Validation of Automated Chromosome Recovery in the Reconstruction of Ancestral Gene Order

Algorithms ◽  
2021 ◽  
Vol 14 (6) ◽  
pp. 160
Author(s):  
Qiaoji Xu ◽  
Lingling Jin ◽  
James H. Leebens-Mack ◽  
David Sankoff
Keyword(s):  
Phylogenetic Tree ◽  
Gene Order ◽  
Evolutionary Process ◽  
Gene Content ◽  
Ancestral Genome ◽  
Maximum Weight ◽  
Ancestral Gene ◽  
Maximum Weight Matching

The RACCROCHE pipeline reconstructs ancestral gene orders and chromosomal contents of the ancestral genomes at all internal vertices of a phylogenetic tree. The strategy is to accumulate a very large number of generalized adjacencies, phylogenetically justified for each ancestor, to produce long ancestral contigs through maximum weight matching. It constructs chromosomes by counting the frequencies of ancestral contig co-occurrences on the extant genomes, clustering these for each ancestor and ordering them. The main objective of this paper is to closely simulate the evolutionary process giving rise to the gene content and order of a set of extant genomes (six distantly related monocots), and to assess to what extent an updated version of RACCROCHE can recover the artificial ancestral genome at the root of the phylogenetic tree relating to the simulated genomes.

scholarly journals Clinical profiles and quality of care of subjects with type 2 diabetes according to their cardiovascular risk: an observational, retrospective study

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Basilio Pintaudi ◽  
Alessia Scatena ◽  
Gabriella Piscitelli ◽  
Vera Frison ◽  
Salvatore Corrao ◽  
...  
Keyword(s):  
Risk Factors ◽  
Type 2 Diabetes ◽  
Quality Of Care ◽  
Cardiovascular Risk ◽  
High Risk ◽  
Cardiovascular Risk Factors ◽  
High Cardiovascular Risk ◽  
Very High

Abstract Background The European Society of Cardiology (ESC) recently defined cardiovascular risk classes for subjects with diabetes. Aim of this study was to explore the distribution of subjects with type 2 diabetes (T2D) by cardiovascular risk groups according to the ESC classification and to describe the quality indicators of care, with particular regard to cardiovascular risk factors. Methods The study is based on data extracted from electronic medical records of patients treated at the 258 Italian diabetes centers participating in the AMD Annals initiative. Patients with T2D were stratified by cardiovascular risk. General descriptive indicators, measures of intermediate outcomes, intensity/appropriateness of pharmacological treatment for diabetes and cardiovascular risk factors, presence of other complications and overall quality of care were evaluated. Results Overall, 473,740 subjects with type 2 diabetes (78.5% at very high cardiovascular risk, 20.9% at high risk and 0.6% at moderate risk) were evaluated. Among people with T2D at very high risk: 26.4% had retinopathy, 39.5% had albuminuria, 18.7% had a previous major cardiovascular event, 39.0% had organ damage, 89.1% had three or more risk factors. The use of DPP4-i markedly increased as cardiovascular risk increased. The prescription of secretagogues also increased and that of GLP1-RAs tended to increase. The use of SGLT2-i was still limited, and only slightly higher in subjects with very high cardiovascular risk. The overall quality of care, as summarized by the Q score, tended to be lower as the level of cardiovascular risk increased. Conclusions A large proportion of subjects with T2D is at high or very high risk. Glucose-lowering drug therapies seem not to be adequately used with respect to their potential advantages in terms of cardiovascular risk reduction. Several actions are necessary to improve the quality of care.

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