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Existence theory and stability analysis of switched coupled system of nonlinear impli...
Rizwan Rizwan
Akbar Zada

Rizwan Rizwan

and 3 more

September 11, 2020
In this paper, we consider switched coupled system of nonlinear implicit impulsive Langevin equations with mixed derivatives. Some sufficient conditions are constructed to observe the existence, uniqueness and generalized Ulam--Hyers--Rassias stability of our proposed model, with the help of Generalized Diaz--Margolis's fixed point approach, over generalized complete metric space. We give an example which supports our main result.
Noninvasive ventilation in physical exercise: what to expect from this therapy?
Emilia Raposo
Paloma Parazzi

Emilia Raposo

and 4 more

September 11, 2020
Noninvasive ventilation, in addition to reducing respiratory work, is a tool to aid physical exercise in individuals with chronic lung diseases. The systematic review aims to demonstrate the benefits and protocols used with NIV associated with physical exercise, its results and the study designs in several lung diseases. A systematic review was carried out using the following databases: Physiotherapy Evidence Database (PEDro), MedLine and Scielo, between January 2015 and April 2020. 64 articles were found in MedLine, of which six were duplicated with the database Peter. Of these 64, eight articles were in accordance with the proposed inclusion criteria, 18 articles were excluded because there was no aerobic exercise during the research; 10 were excluded due to access to the abstract only; one study did not make use of NIV during the proposed exercise. 11 articles were listed for analysis. The studies analyzed in the present review demonstrate that the immediate and concomitant use of NIV before or during exercise, improved lung function in patients with chronic lung disease, heart failure and neurological patients, in addition to improving the distance covered by the walking test. six minutes in children and adolescents.
Effect of Initial Crack-depth Ratio on Dynamic Fracture Properties of FRP Strengthene...
Jueding Liu
fnq xiangqian

Jueding Liu

and 2 more

September 11, 2020
Abstract: In order to study the dynamic fracture properties of FRP strengthened concrete, the three-point bending experiment of FRP strengthened concrete beams with five different initial crack-depth ratios was carried out by using MTS-810 hydraulic servo experiment machine. The initial crack-depth ratios are 0.2, 0.3, 0.4, 0.5 and 0.6 respectively. The effects of different initial crack-depth ratios on the load-crack mouth opening displacement (CMOD) curves, failure process, increment of critical crack-depth ratio and flexibility coefficient of FRP strengthened concrete beams were analyzed through displacement controlled monotonic loading method. Combined with Pearson correlation experiment formula, the correlation between initial crack-depth ratios and different fracture parameters was quantitatively analyzed. The conclusions could be drawn that, there are three obvious critical points in the fracture damage process of FRP strengthened concrete beams: the starting point of concrete crack, the first peak point and the ultimate bearing capacity point. As the increase of initial crack-depth ratios, the crack initiation load decreases, but the first peak load and ultimate load increase first and then decrease. It is found that the stress intensity factors (SIFs) of the three critical points increase first and then decrease with the increase of the initial crack-depth ratio, and when initial crack-depth ratio of concrete beams is 0.4, three kinds of SIF all reach the maximum value. The increment of critical crack-depth ratio and flexibility coefficient of FRP strengthened concrete beams are related to initial crack-depth ratio, which could be used to reflect the effect of initial crack-depth ratio on the deformation capacity of concrete specimens. Keywords: FRP strengthened concrete; dynamic fracture; initial crack-depth ratios; stress intensity factors; increment of critical crack-depth ratio; flexibility coefficient
Identification of immunological, inflammatory, hematological, and coagulation abnorma...
Rundong Qin
Li He

Rundong Qin

and 14 more

September 11, 2020
Background: Laboratory abnormalities associated with disease severity and mortality in patients with coronavirus disease 2019 (COVID-19) have been reported in many observational studies. However, there are significant heterogeneities in patient characteristics and research methodologies in these studies. Objectives: We aimed to provide an updated synthesis of the association between laboratory abnormalities and COVID-19 prognosis. Methods: We conducted an electronic search of PubMed, Scopus, Ovid, Willey, Web of Science, and the China National Knowledge Infrastructure (CNKI) for studies reporting hematological, coagulation, inflammatory, and immunological results during hospital admission of COVID-19 patients with different severities and outcomes. Results: A total of 64 studies were included in the current meta-analysis, with 8 hematological, 3 coagulation, 5 inflammatory, and 23 immunological variables reported. Of them, white blood cell (WBC) and neutrophil counts, D-dimer level, procalcitonin (PCT), erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), ferretin, serum amyloid A (SAA), interleukins (ILs)–2R, IL-6, and IL-10 were significantly increased in severely ill patients and non-survivors. Meanwhile, non-severely ill patients and survivors presented significantly higher counts of eosinophils, lymphocytes, and CD4+ and CD8+ T cells. Conclusions: The current meta-analysis provides a comprehensive and updated synthesis of the association between admission laboratory abnormalities with severity and mortality of COVID-19. Our results highlight that increases in the levels of PCT, ESR, CRP, ferretin, SAA, IL-2R, IL-6, and IL-10 were associated with disease deterioration, whereas elevated eosinophils, lymphocytes, and T-cell subsets might serve as indicators of favorable outcomes.
The Analysis of Left Ventricular Ejection Fraction after Minimally Invasive Surgery f...
Yukiharu Sugimura
Shintaro Katahira

Yukiharu Sugimura

and 12 more

September 11, 2020
Background: Although minimally invasive mitral valve surgery (MIMVS) has become the first choice for primary mitral regurgitation (MR) in recent years, clinical evidence in this field is yet limited. The main focus of this study was the analysis of preoperative (Pre), postoperative (Post) and 1-year follow-up (Fu) data in our series of MIMVS in order to identify factors that have an impact on the left ventricular ejection fraction (LVEF) evolution after MIMVS. Methods: We reviewed the perioperative and 1-year follow-up data from 436 patients with primary MR (338 isolated MIMVS und 98 MIMVS combined with tricuspid valve repair) to analyzed patients baseline characteristics, the change of LV size, the postoperative evolution of LVEF and its factors, and the clinical outcomes. Results: The overall mean value of EF slightly decreased at 1-year follow-up (mean change of LVEF: -2.63±9.00%). A significant correlation was observed for PreEF und EF evolution, the higher PreEF the more pronounced decreased EF evolution (in all 436 patients; r= -0.54, p<0.001, in isolated MIMVS; r= -0.54, p<0.001, in combined MIMVS; r= -0.53, p<0.001). Statistically significant differences for negative EF evolution were evident in patients with mild or greater tricuspid valve regurgitation (TR) (in all patients; p<0.05, OR=1.64, in isolated MIMVS; p<0.01, OR=1.93, respectively). Overall clinical outcome in NYHA classification at 1 year was remarkably improved. Conclusions: Our results suggest an excellent clinical outcome at 1 year, although mean LVEF slightly declined over time. TR could be a predictor of worsened FuEF in patients undergoing MIMVS.
Analytical modeling of plastic strain induced by deep rolling
kunpeng han

kunpeng han

September 11, 2020
To evaluate the through depth plastic strain generated by deep rolling, the analytical model of plastic strain was developed based on the Hertz contact theory. The analytical model of plastic strain was verified by numerical simulation. Then, the effect of rolling force, the diameter of the ball and ball material on the through depth plastic strain was investigated and validated by the through depth microhardness profiles. The results show that first method of the analytical model is more accurate, and the error of maximum plastic strain derived by the analytical model and finite element (FE) simulation is just 7.8%. The through depth and relevant effective depth increase with the increase of rolling force; the through depth plastic strain decreases with increasing diameter of the ball. The tungsten carbide ball induces more plastic strain than the ball made of silicon nitride and steel. Moreover, the plastic strain profiles are in line with the variation of microhardness along with the depth.
Mathematical Approach to Compute the Molecular Composition of HTL-derived Renewable C...
Vishwas Prabhu
Nikhlesh Saxena

Vishwas Prabhu

and 5 more

September 11, 2020
To assess the techno-economic screening of HTL oil for various feedstock, it is crucial to have information on molecular composition of the feed and products. There are limitations of existing analytical methods to identify and quantify all the molecules present in the bio-fuel. Therefore, there is a need to find alternate ways to quantify the molecular composition of feed and expected products. The modelling work on bio-oil is developed based on a mathematical approach using simple analytical results like CHNO along with structural analysis of oil like FTIR, NMR analysis for HTL derived oil from microalgae. This mathematical framework is further extended to predict the molecular composition of HTL-oil obtained from feedstocks like mixed plastic waste, sludge etc. A multi-dimensional molecular matrix is developed based on the distributions of side chains, aromatic rings, and olefinic carbon on top of core molecules. Optimum parameters are found using appropriate optimization algorithms.
Absorption of Nitric Oxide in Simulated Flue Gas by Azole-Based Hydrophobic Deep Eute...
Ying Sun
Minjie Gao

Ying Sun

and 5 more

September 11, 2020
Functional hydrophobic deep eutectic solvents composed with azoles as hydrogen bond donors, and [N8881]Cl and [N8881]Br as hydrogen bond acceptors were designed and synthesized to absorb low concentrations NO. The good hydrophobicity reduces the cost of operating effectively. Moreover, the capacity of 10 vol % NO absorption by Im-[N8881]Cl DES can reach 3.91 mol NO / mol Im at 40 oC. Besides, Im-[N8881]Cl DES can be regenerated, and the absorption capacity of NO by the regenerated Im-[N8881]Cl DES shows no significant loss for at least 5 recycles. FTIR and 1H NMR were used to verify the mechanism. The results indicate that there is chemical interaction between NO and Im-[N8881]Cl DES and the main chemical active sites are N (2) and N (5) on Im by forming NONOates. This series of hydrophobic, efficient and reversible NO absorbents may provide a new idea for NO capture technique.
Factors underlying to increased prevalence of Pythium disease following non-targeted...
Huizhu Yuan
Xiujun Tang

Huizhu Yuan

and 5 more

September 11, 2020
Microbial communities are essential for soil health, but fungicide application can have major effects on their structure, and it is difficult to predict whether non-target pathogens in the soil will cause major crop damage. Using collected soil with a history of poor corn (Zea mays) seedling emergence, we demonstrate that the poor emergence of corn seedlings from seeds coated with the fungicide tebuconazole is primarily due to infection of surviving soil pathogens, particularly Pythium complexes that are not targeted by fungicide tebuconazole. We determined that the bases for the increased infection by non-target species of Pythium were: 1) the selective fungicidal activity of seed-applied tebuconazole showed a low level of control against Pythium species but had a significant effect on soil fungi, thereby releasing Pythium spp. from competition with other soil microorganisms; 2) the growth of the natural enemies in soil, Trichoderma spp., was strongly inhibited by tebuconazole; and 3) low temperature was the key factor of triggering fatal injury of Pythium pathogens to corn seeds. Taken together, the non-target effects of tebuconazole are likely not significant under favorable plant growing conditions, but are considerable as a result of low temperature stress.
Semi-analytical multiple solutions for nanofluid flow and heat transfer past a shrink...
Hashim Hashim
Muhammad  Hafeez

Hashim Hashim

and 1 more

September 11, 2020
A considerable amount of the energy consumption has indeed been affected in industry by friction and inefficient heat transfer. One promising way of overcoming this deficiency of ordinary heat transferring fluids is to use the nanoparticles. Recently, several studies have documented that nanofluid, formed by adding the nanoparticles to the base fluid, can significantly improve the thermal efficiency of these base fluids. In this communication, we present a numerical study for two-dimensional flow of Graphene-oxide (GO)/water nanofluids generated by a stretching/shrinking surface in the presence of porous media. The heat transfer analysis is further investigated under the influence of second order partial slip and mass suction. The current problem is governed by a system of partial differential equations which are derived using conservation laws and Boussinesq-approximations. These non-linear governing equations are converted into a set of ordinary differential equations with the help of similarity transformations. Multiple solutions are achieved analytically for flow fields while numerically for temperature fields. Numerical simulations are conducted using boundary value problem solver (bvp4c) in MATLAB. The influences of various physical parameters, for instance, nanoparticles volume fraction, porosity parameter, suction parameter, first and second-order slip parameters as well as Prandtl number on momentum and thermal boundary layers are presented graphically in detail. It is observed that the solution domain is significantly widen by increasing the nanoparticles volume fraction.
Performance of a degassing hydrocyclone with main and subsidiary chambers
Xiao Xu
Junjie Wang

Xiao Xu

and 4 more

September 11, 2020
Based on the premise that large bubbles are removed in larger cyclones and small bubbles are removed in smaller cyclones, a combined degassing hydrocyclone with main and subsidiary chambers was designed to enhance liquid degassing. The liquid feed volume flow rate ranged from 0.377 to 1.459 m3/h, and the gas feed volume flow rate ranged from 0.197 to 1.000 m3/h. The pressure loss, liquid flow rate at the gas outlet, split ratio, gas flow rate at the liquid outlet and degassing efficiency of the degassing hydrocyclone were measured and calculated. Correlative equations for pressure loss and degassing efficiency were established. The experimental results show that the degassing hydrocyclone can remove most of the gas and has good degassing performance in a large gas-liquid flow rate range. The parameter contours provide an effective foundation for the removal of gas from industrial fluids.
Machine Learning Applied to Ultrasonic Flow Meters for measuring Dilute, Turbulent Wa...
Thiam Wan
Hon Chung Lau

Thiam Wan

and 2 more

September 11, 2020
An ultrasonic flow meter that is calibrated in single phase flow has inherent errors when applied to measure dilute water-bentonite mixture flow. This paper endeavors to use artificial intelligence for recalibration of an ultrasonic flow meter. A commercial ultrasonic transit time flow meter was tested for measuring dilute water-bentonite mixture flow of 0.1-1.0 vol% concentration at room temperature. Results show the test data had a systematic error of -8.3% and a random error of 20.3%. The machine learning LLS regression,2D interpolation and Gaussian Naïve Bayes methods were considered in this exercise. Finally, a combined 2D interpolation method and Gaussian Naïve Bayes classifier approach was preferred. It reduced the systematic error to -0.6% and random errors to ±13.7%. Our study shows a high accuracy ultrasonic flow meter with systematic errors smaller than 1% for oil and gas multiphase application is possible with the aid of artificial intelligence technology.
Pilot drug and therapeutic committee program in Sierra Leone: a descriptive mixed met...
John  Kabba
Mark Koroma

John Kabba

and 9 more

September 11, 2020
Introduction Irrational medicine use is proportionately higher in low and middle-income countries like Sierra Leone. This study aims at exploring the structure, functions, and challenges of Drug, and Therapeutics Committees (DTC) recently piloted in Sierra Leone. Method A two-phase mixed-method study design was used in this study. Firstly, a cross-sectional survey using an online questionnaire to assess the structure, indicators, and challenges of DTC . In phase two, a semi-structured interview was used to get deeper insights into the key issues that emerged from the survey. Participants were mainly pharmacists in-charge at the hospitals where the DTC program hasbeen established. MS Excel 2019 and NVivo version 12 were respectively used for data management and analysis. Results DTCs mostly had a minimum of ten members consisting of a mix of both medical and hospital administrative staff. The main functions of DTC are ensuring rational medicines use, monitoring, and reporting adverse drug reactions. All but one hospital had subcommittees that are either effective or nonfunctional. The main challenges in DTC functions and maintenance were funding (n=6), DTC decision implementation (n=4), and unmotivated members (n=4). Strategies suggested to improve DTC at public hospitals and nationwide include; resource allocation, monitoring, and evaluating DTC functions and capacity building of its members. Conclusion DTC present a compelling opportunity towards achieving rational medicines use at the hospital level in Sierra Leone. Nonetheless, lack of funding, operational resources, are significant limitations. Policymakers must note these drawbacks whilst expanding DTC programs to other hospitals in Sierra Leone.
Probable drug-induced liver injury with kedaling tablets : A case report and systemat...
jiabing wang

jiabing wang

September 11, 2020
Kedaling tablets is an extract of with Corydalis yanhusuo W.T. Wang and used to coronary heart disease, angina pectoris, myocardial infarction with no previously well documented hepatotoxicity. We report the first case of kedaling tablets-related drug-induced liver injury (DILI), which highlights the need for clinician awareness regarding potential hepatotoxicity of kedaling tablets, particularly among patients with pre-existing liver disease.
Comparison Between Mostly-Used Old-Fashion Method and New PITOPS Simulator for PID Co...
Lalit Kumar

Lalit Kumar

September 11, 2020
Since the 1980’s the field of process control has become increasingly important in chemical and petrochemical plants, oil refineries and other manufacturing units. They are widely used are & still a very powerful tool in process control domain is the PID controller. To get optimal performance of any PID controller and to extract the full economic and safety benefits of it, appropriate PID tuning is required. This paper examines and compares industrial mostly-used old-fashion PID controller tuning method with the better PITOPS simulator. Old-fashion PID controller tuning method use Trail-and-Error approach or Empirical sets of rules, whereas the PITOPS technology uses powerful mathematical NC-GRG (Nonlinear Constrained General Reduced Gradient) optimization approach developed by International automation and process control company PiControl Solutions. The main goal of the paper is to highlight the benefits of PITOPS over the mostly-used old-fashion methods for industrial PID controller tuning, over several typical examples.
Diet-induced obesity aggravates NK cell-mediated contact hypersensitivity reaction in...
Paulina Kowalczyk
Monika Majewska-Szczepanik

Paulina Kowalczyk

and 4 more

September 11, 2020
BACKGROUND: Previous studies showed that liver NK cells mediate contact hypersensitivity (CHS) reaction in mice. There are many reports showing that obesity is accompanied with chronic low-grade inflammation and it promotes several inflammatory diseases. It was shown that diet-induced obesity (DIO) aggravates classical T cell-mediated CHS in C57BL/6 mice. Our work sheds light on a poorly explored subject of the influence of DIO on the course of NK cell-mediated CHS reaction in mice. METHODS: We evaluated the effect of DIO on NK cell-mediated CHS reaction using a model of dinitrofluorobenzene (DNFB)-induced CHS in Rag1-/- mice. RESULTS: Our data show that mice fed HFD for 8 but not for 4 weeks developed aggravated CHS reaction determined by ear swelling measurement when compared to animals kept on normal diet (ND) prior to DNFB sensitization. The obese Rag1-/- mice presented the adipose tissue inflammation. Furthermore, in vitro analysis showed that feeding with HFD significantly increases IFN-γ and IL-12p70 and decreases adiponectin concentration in liver mononuclear cells (LMNC) culture supernatants. The flow cytometry analysis of LMNC revealed that HFD treatment prior to DNFB sensitization increases the percentage of NK1.1+IFN-γ+ cell population and affects development and maturation of NK1.1+ cells. CONCLUSION: In summary, current results suggest that the DIO significantly modulates the local and systemic inflammatory response, contributing to exacerbation of the CHS response mediated by liver NK cells.
Seeking the ‘point of no return’ in the sequence of events leading to mortality of ma...
Yakir Preisler
Fedor Tatarinov

Yakir Preisler

and 3 more

September 11, 2020
Drought-related tree mortality is increasing globally, but the sequence of events leading to it remains poorly understood. To identify such sequence, we used a 2016 tree mortality event in the semi-arid pine forest of Yatir were dendrometry and sap flow measurements were carried out in 31 trees, of which seven died. A comparative analysis revealed three stages leading to mortality. First, a decrease in tree diameter in all dying trees, but not in the living ones, eight months ‘prior to the visual signs of mortality’ (PVSM; e.g., brown needles). Second, a decay to near zero in the diurnal stem swelling/shrinkage dynamics, reflecting the loss of stem radial water flow in the dying trees, six months PVSM. Third, cessation of stem sap flow three months PVSM. Eventual mortality could therefore be detected long before visual signs are observed, and the three stages identified here demonstrated the differential effects of drought on stem growth, water storage capabilities, and soil water uptake. The results indicated that breakdown of radial stem water flow and phloem functionality is a critical element in defining the ‘point of no return’ in the sequence of events leading to mortality of mature trees.
Effect of air-pollutants and environmental factors on COPD exacerbations: time series...
Jong Seung Kim
Hyu Seok  Shin

Jong Seung Kim

and 8 more

September 11, 2020
Background: Chronic obstructive pulmonary disease (COPD) exacerbation (CE) is characterized by the rapid deterioration of respiratory symptoms caused by air pollution, but there have been no comprehensive studies with regard to the age-stratified effect of air pollution. We investigate the short-term effects of air pollution and environmental factors on CE. Methods: By merging the individualized environmental data and Korea’s National Health Insurance cohort, we conducted Quasi-Poisson analysis to evaluate the effects of air pollutants and environmental factors on CE. Results: From January 2007 to December 2012, a total of 15110 CE events occurred, which showed seasonal dynamics in CE events, air pollutants (particulate matter less than 10 µm (PM10), NO2, SO2) and environmental factors (wind speed (WS), solar sunshine (SS)). The only factor affecting CE was PM10, and this occurred on lag days 4, 5, and 6 and had a peak hazard ratio (HR) of 1.0404 on lag day 5. PM10 also had a lag-cumulative effect on CE risk from lag day 6 to lag day 10. In subgroup analysis on age and level of parameters, each factor had a different significant effect on CE on different lag days. Conclusions: PM10 uniquely affects CE at lag-specific day 5 (from lag day 4 to lag day 6). PM10 also had a lag-cumulative effect on CE risk which showed a pattern proportional to the concentration of PM10. Considering the subgroup analysis, we need to devise different strategies for air pollutants and age for patients with COPD exacerbation.
Depurazione delle acque reflue: controllo dei contaminanti emergenti 
Antonello Nigro

Antonello Nigro

October 20, 2020
L’inquinamento dell’uomo verso la natura avviene su molti fronti: uno di questo è la contaminazione delle acque reflue urbane con prodotti farmaceutici. Dei semplici prodotti per l’igiene e dei comuni farmaci utilizzati quotidianamente per curare sintomi come febbre, infiammazioni e dolori vari, possono causare effetti nocivi agli organismi acquatici. Tali contaminanti possono provocare alterazioni del sistema endocrino ed un incremento della resistenza microbica ai farmaci. Infatti sempre di più si riscontrano tracce di contaminanti emergenti, cioè sulfametossazolo (SMX), diclofenac (DFC) e carbamazepina (CBZ), negli effluenti delle acque reflue, nei fiumi, laghi, mari e nell’acqua potabile.  L’obiettivo di questo studio è di valutare il livello di efficienza di alcune tecniche avanzate di rimozione di contaminati emergenti attraverso processi di ossidazione avanzata (AOP). 
Spermatophyta timetree, accelerated base substitution rates at mid-Cretaceous and the...
Soichi Osozawa
Cunio Nackejima

Soichi Osozawa

and 2 more

September 11, 2020
We constructed a whole of Spermatophyta timetree by employing BEAST v1. X applying the nuclear ribosomal ITS, and chloroplastic matK and rbcL. Robust multipoint calibrations were done by applying fossil ages up to the Jurassic for 20 genera and a Quaternary geological event age of 1.55 Ma for 6 genera. The resultant topology was concordant to the APG system, and we successfully and precisely dated the phylogeny. Through the BEAST analyses, we discovered the exponential increase in base substitution rate in recent geologic time, and suggested that a potential cause was generation of C4 plants and the triggered Quaternary climatic change. The raised rate might have resulted in the increasing of Spermatophyta diversity including endemic Asarum and Viola species. Another rise of base substitution rate was found around 120 Ma, reflecting the order level radiation and diversification of Angiospermae at the middle Cretaceous time.
Variation of the wax deposit properties in radial direction in crude oil pipeline
Kaifeng Fan
Si Li

Kaifeng Fan

and 2 more

September 11, 2020
The variations of wax deposit properties in radial direction in crude oil pipe were investigated through flow-loop experiments. It was found that the wax content and wax appearance temperature (WAT) of the surface deposit were lower than those at bottom. Ranked from high to low, the mass ratio of wax molecules heavier than the critical carbon number (CCN) is the bottom deposit, surface deposit and crude oil, while in the range lighter than the CCN, the order is just opposite. Microscopic observations indicated larger amount and more rod-like wax crystals existed in the bottom layer. Moreover, the bottom deposit was stronger in structure and presented higher yield stress than the surface deposit. The present work revealed and verified the significant differences in the radial properties of the wax deposits, which should be considered in future studies, especially with regard to the force on the pig.
SimBit: A high performance, flexible and easy-to-use population genetic simulator
Remi Matthey-Doret

Remi Matthey-Doret

September 11, 2020
SimBit is a general purpose and high performance forward-in-time population genetics simulator. SimBit has been designed to be able to model a wide diversity of complex scenarios from a simple set of commands that are very flexible. SimBit also comes with a R wrapper that simplifies the management of an entire research project from the creation of a grid of parameters and corresponding inputs, running simulations and gathering outputs for analysis. Implementing various representations of the individual’s genotype allows SimBit to sustain a high performance in a wide diversity of simulation scenarios. SimBit’s performance was extensively benchmarked in comparison to SLiM, Nemo and SFS_CODE. No single program systematically outperforms the others but SimBit is most often the highest performing program and maintains high performance in all scenarios considered.
MultiGWAS: An integrative tool for Genome Wide Association Studies (GWAS) in tetraplo...
Luis Garreta
Ivania Cerón-Souza

Luis Garreta

and 3 more

September 11, 2020
The Genome-Wide Association Studies (GWAS) are essential to determine the genetic bases of either ecological or economic phenotypic variation across individuals within populations of model and non-model organisms. For this research question, current practice is the replication of the GWAS testing different parameters and models to validate the reproducibility of results. However, straightforward methodologies that manage both replication and tetraploid data are still missing. To solve this problem, we designed the MultiGWAS, a tool that does GWAS for diploid and tetraploid organisms by executing in parallel four software, two for polyploid data (GWASpoly and SHEsis) and two for diploids data (PLINK and TASSEL). MultiGWAS has several advantages. It runs either in the command line or in an interface. It manages different genotype formats, including VCF. It executes both the full and naïve models using several quality filters. Besides, it calculates a score to choose the best gene action model across GWASPoly and TASSEL. Finally, it generates several reports that facilitate the identification of false associations from both the significant and the best-ranked association SNP among the four software. We tested MultiGWAS with tetraploid potato data. The execution demonstrated that the Venn diagram and the other companion reports (i.e., Manhattan and QQ plots, heatmaps for associated SNP profiles, and chord diagrams to trace associated SNP by chromosomes) were useful to identify associated SNP shared among different models and parameters. Therefore, we confirmed that MultiGWAS is a suitable wrapping tool that successfully handles GWAS replication in both diploid and tetraploid organisms.
The future of next generation sequencing datasets: technological shifts provide oppor...
Rishi De-Kayne
David Frei

Rishi De-Kayne

and 5 more

September 11, 2020
Technological advances in DNA sequencing over the last decade now permit the production and curation of large genomic datasets in an increasing number of non-model species. Additionally, this new data provides the opportunity for combining datasets, resulting in larger studies with a broader taxonomic range. Whilst the benefits of new sequencing platforms are obvious, shifts in sequencing technology can also pose challenges for those wishing to combine new sequencing data with data sequenced on older platforms. Here, we outline the types of studies where the use of curated data might be beneficial, and highlight potential biases that might be introduced by combining data from different sequencing platforms. As an example of the challenges associated with combining data across sequencing platforms, we focus on the impact of the shift in Illumina's base calling technology from a four-channel to a two-channel system. We caution that when data is combined from these two systems, erroneous guanine base calls that result from the two-channel chemistry can make their way through a bioinformatic pipeline, eventually leading to inaccurate and potentially misleading conclusions. We also suggest solutions for dealing with such potential artifacts, which make samples sequenced on different sequencing platforms appear more differentiated from one another than they really are. Finally, we stress the importance of archiving tissue samples and the associated sequences for the continued reproducibility and reusability of sequencing data in the face of ever-changing sequencing platform technology.
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