Abstract
The Molecular Evolutionary Genetics Analysis (MEGA) software has matured to contain a large collection of methods and tools of computational molecular evolution. Here, we describe new ...additions that make MEGA a more comprehensive tool for building timetrees of species, pathogens, and gene families using rapid relaxed-clock methods. Methods for estimating divergence times and confidence intervals are implemented to use probability densities for calibration constraints for node-dating and sequence sampling dates for tip-dating analyses. They are supported by new options for tagging sequences with spatiotemporal sampling information, an expanded interactive Node Calibrations Editor, and an extended Tree Explorer to display timetrees. Also added is a Bayesian method for estimating neutral evolutionary probabilities of alleles in a species using multispecies sequence alignments and a machine learning method to test for the autocorrelation of evolutionary rates in phylogenies. The computer memory requirements for the maximum likelihood analysis are reduced significantly through reprogramming, and the graphical user interface has been made more responsive and interactive for very big data sets. These enhancements will improve the user experience, quality of results, and the pace of biological discovery. Natively compiled graphical user interface and command-line versions of MEGA11 are available for Microsoft Windows, Linux, and macOS from www.megasoftware.net.
Abstract
The Molecular Evolutionary Genetics Analysis (MEGA) software enables comparative analysis of molecular sequences in phylogenetics and evolutionary medicine. Here, we introduce the macOS ...version of the MEGA software. This new version eliminates the need for virtualization and emulation programs previously required to use MEGA on Apple computers. MEGA for macOS utilizes memory and computing resources efficiently for conducting evolutionary analyses on macOS. It has a native Cocoa graphical user interface that is programmed to provide a consistent user experience across macOS, Windows, and Linux. MEGA for macOS is available from www.megasoftware.net free of charge.
We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major ...upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable ...cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
•Nanomaterial deposition on heating surface are used to attain reduction in wall superheat, enhancing nucleate boiling HTC and CHF.•Different working fluid is used such as de-ionized water, ...fluorocarbon fluid, hydofluoroethers and refrigeration-based fluid for enhancing CHF.•The surface modification enhanced the CHF due to the reduction in wall superheat temperature, increased nucleation site, porosity rise, enhanced surface wettability, small nano-pores/cavities generation, rise in bubble release frequency.•Nanoparticle size, nanofluid preparation techniques and concentration of nanofluid mainly influenced the CHF.
Boiling is the most significant phase change phenomena for various applications such as cooling of electronic devices, heat pipes, cooling in nuclear reactor, different industrial application and plenty more. Due to its wide scope of application, any enhancement in this domain leads to remarkable economic and energy efficient consequences. Augmentations in boiling heat transfer performance are very crucial which establishes the various industrial applications further energy efficient. To reduce the energy dissipation in heat transfer equipment, boiling heat transfer augmentation is one of the significant techniques used by researchers. This paper demonstrates a thorough review and investigation of published articles describing the various surface modification method (nanomaterial coating, nano/micro porous coating, nano/micro structured surface) for pool boiling and flow boiling heat transfer enhancement as well as the effect of surface modification on wettability, porosity, surface roughness, nucleation sites are studied. Various augmentation methods are utilized to attain three apparent heat transfer desire: reducing wall superheat temperature, enhancing pool boiling heat transfer coefficient (HTC) and improving critical heat flux (CHF).
•There is moderate awareness related to transmission and symptoms of COVID-19 among educated population in India.•There is adequate awareness among public regarding preventive measures for COVID-19 ...infection.•There is a positive attitude of public towards social-distancing, avoiding party and travel and maintaining hygiene.•People report anxiety, worries, paranoia about acquiring infection and sleep disturbances during this pandemic.•More the 80 % people perceive mental healthcare need to deal with their issues during this COVID-19 pandemic.
Novel Corona Virus Disease (COVID-19) originating from China has rapidly crossed borders, infecting people throughout the whole world. This phenomenon has led to a massive public reaction; the media has been reporting continuously across borders to keep all informed about the pandemic situation. All these things are creating a lot of concern for people leading to heightened levels of anxiety. Pandemics can lead to heightened levels of stress; Anxiety is a common response to any stressful situation. This study attempted to assess the knowledge, attitude, anxiety experience, and perceived mental healthcare need among adult Indian population during the COVID-19 pandemic. An online survey was conducted using a semi-structured questionnaire using a non-probability snowball sampling technique. A total of 662 responses were received.
The responders had a moderate level of knowledge about the COVID-19 infection and adequate knowledge about its preventive aspects. The attitude towards COVID-19 showed peoples' willingness to follow government guidelines on quarantine and social distancing. The anxiety levels identified in the study were high. More than 80 % of the people were preoccupied with the thoughts of COVID-19 and 72 % reported the need to use gloves, and sanitizers. In this study, sleep difficulties, paranoia about acquiring COVID-19 infection and distress related social media were reported in 12.5 %, 37.8 %, and 36.4 % participants respectively. The perceived mental healthcare need was seen in more than 80 % of participants. There is a need to intensify the awareness and address the mental health issues of people during this COVID-19 pandemic.
Evolutionary information on species divergence times is fundamental to studies of biodiversity, development, and disease. Molecular dating has enhanced our understanding of the temporal patterns of ...species divergences over the last five decades, and the number of studies is increasing quickly due to an exponential growth in the available collection of molecular sequences from diverse species and large number of genes. Our TimeTree resource is a public knowledge-base with the primary focus to make available all species divergence times derived using molecular sequence data to scientists, educators, and the general public in a consistent and accessible format. Here, we report a major expansion of the TimeTree resource, which more than triples the number of species (>97,000) and more than triples the number of studies assembled (>3,000). Furthermore, scientists can access not only the divergence time between two species or higher taxa, but also a timetree of a group of species and a timeline that traces a species' evolution through time. The new timetree and timeline visualizations are integrated with display of events on earth and environmental history over geological time, which will lead to broader and better understanding of the interplay of the change in the biosphere with the diversity of species on Earth. The next generation TimeTree resource is publicly available online at http://www.timetree.org.
RelTime estimates divergence times by relaxing the assumption of a strict molecular clock in a phylogeny. It shows excellent performance in estimating divergence times for both simulated and ...empirical molecular sequence data sets in which evolutionary rates varied extensively throughout the tree. RelTime is computationally efficient and scales well with increasing size of data sets. Until now, however, RelTime has not had a formal mathematical foundation. Here, we show that the basis of the RelTime approach is a relative rate framework (RRF) that combines comparisons of evolutionary rates in sister lineages with the principle of minimum rate change between evolutionary lineages and their respective descendants. We present analytical solutions for estimating relative lineage rates and divergence times under RRF. We also discuss the relationship of RRF with other approaches, including the Bayesian framework. We conclude that RelTime will be useful for phylogenies with branch lengths derived not only from molecular data, but also morphological and biochemical traits.
Fine ambient aerosols (PM2.5) levels in the atmosphere are continuously worsening over Delhi and National Capital Region (NCR) of India. Complete source profiles are required to be assessed for ...implementation of proper mitigation measures over the NCR. In this study, emission sources of PM2.5 are reported for the NCR of India for samples collected during December 2016 to December 2017 at three sampling sites in Delhi, Uttar Pradesh and Haryana. Organic constituents (n-alkanes, isoprenoid hydrocarbons, polycyclic aromatic hydrocarbons, phthalates, levoglucosan and n-alkanoic acids) in PM2.5 were measured to apportion the sources over the study area. Source apportionment of PM2.5 was performed using organic constituents by Positive Matrix Factorization (PMF) and Principal Component Analysis (PCA). Health risk associated with organic pollutants PAHs and carcinogen BEHP bis(2-ethylhexyl) phthalate demonstrated the threat of PM2.5 exposure via inhalation. Transport pathways of air masses were evaluated using 3-day backward trajectories and observed that some air masses originated from local sources along with long-range transport which influenced the PAHs concentration during most of the study period over the NCR. PMF and PCA resulted in the five major emission sources vehicular emissions (32.2%), biomass burning (30%), cooking emissions (16.8%), plastic burning (13.4%), mixed sources (7.6%) including biogenic and industrial emissions for PM2.5 over the sampling sites. The present study reveals that transport sector is a major source to be targeted to reduce the vehicular emissions and consequent health risks associated with organic pollutants especially PAHs.
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•Emission sources of PM2.5 are reported for three sites in the NCR of India.•Source apportionment was performed using PMF and PCA.•Health risk assessment for organic constituents suggests implementation of effective reduction strategies.•Cluster analysis showed influence of transport routes of air masses on levels of organic constituents at receptor sites.
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