scholarly journals Phylogenomics invokes the clade housing Cryptista, Archaeplastida, and Microheliella maris

2021 ◽  
Author(s):  
Euki Yazaki ◽  
Akinori Yabuki ◽  
Ayaka Imaizumi ◽  
Keitaro Kume ◽  
Tetsuo Hashimoto ◽  
...  
Keyword(s):  
Large Scale ◽  
Phylogenetic Signal ◽  
Taxon Sampling ◽  
Secondary Endosymbiosis ◽  
The Novel ◽  
Sister Relationship ◽  
Homologous Genes ◽  
Gene Alignment ◽  
Red Algal ◽  
Algal Endosymbiont

AbstractAs-yet-undescribed branches in the tree of eukaryotes are potentially represented by some of “orphan” protists (unicellular micro-eukaryotes), of which phylogenetic affiliations have not been clarified in previous studies. By clarifying the phylogenetic positions of orphan protists, we may fill the previous gaps in the diversity of eukaryotes and further uncover the novel affiliation between two (or more) major lineages in eukaryotes. Microheliella maris was originally described as a member of the phylum Heliozoa, but a pioneering large-scale phylogenetic analysis failed to place this organism within the previously described species/lineages with confidence. In this study, we analyzed a 319-gene alignment and demonstrated that M. maris represents a basal lineage of one of the major eukaryotic lineages, Cryptista. We here propose a new clade name “Pancryptista” for Cryptista plus M. maris. The 319-gene analyses also indicated that M. maris is a key taxon to recover the monophyly of Archaeplastida and the sister relationship between Archaeplastida and Pancryptista, which is collectively called as “CAM clade” here. Significantly, Cryptophyceae tend to be attracted to Rhodophyta depending on the taxon sampling (ex., in the absence of M. maris and Rhodelphidia) and the particular phylogenetic “signal” most likely hindered the stable recovery of the monophyly of Archaeplastida in previous studies. We hypothesize that many cryptophycean genes (including those in the 319-gene alignment) recombined partially with the homologous genes transferred from the red algal endosymbiont during secondary endosymbiosis and bear a faint phylogenetic affinity to the rhodophytan genes.

Covalent Atomic Bridges Enable Unidirectional Enhancement of Electronic Transport in Aligned Carbon Nanotubes

2019 ◽  
Author(s):  
Mingguang Chen ◽  
Wangxiang Li ◽  
Anshuman Kumar ◽  
Guanghui Li ◽  
Mikhail Itkis ◽  
...  
Keyword(s):  
Carbon Nanotubes ◽  
Electrical Transport ◽  
Large Scale ◽  
The Novel ◽  
Electrical Measurements ◽  
Metal Atoms ◽  
Aligned Carbon Nanotubes ◽  
Transport Channels ◽  
Walled Carbon Nanotubes ◽  
Bulk Structures

<p>Interconnecting the surfaces of nanomaterials without compromising their outstanding mechanical, thermal, and electronic properties is critical in the design of advanced bulk structures that still preserve the novel properties of their nanoscale constituents. As such, bridging the p-conjugated carbon surfaces of single-walled carbon nanotubes (SWNTs) has special implications in next-generation electronics. This study presents a rational path towards improvement of the electrical transport in aligned semiconducting SWNT films by deposition of metal atoms. The formation of conducting Cr-mediated pathways between the parallel SWNTs increases the transverse (intertube) conductance, while having negligible effect on the parallel (intratube) transport. In contrast, doping with Li has a predominant effect on the intratube electrical transport of aligned SWNT films. Large-scale first-principles calculations of electrical transport on aligned SWNTs show good agreement with the experimental electrical measurements and provide insight into the changes that different metal atoms exert on the density of states near the Fermi level of the SWNTs and the formation of transport channels. </p>

scholarly journals IoT Traffic: Modeling and Measurement Experiments

IoT ◽  
2021 ◽  
Vol 2 (1) ◽  
pp. 140-162
Author(s):  
Hung Nguyen-An ◽  
Thomas Silverston ◽  
Taku Yamazaki ◽  
Takumi Miyoshi
Keyword(s):  
Smart Home ◽  
Large Scale ◽  
Traffic Modeling ◽  
The Novel ◽  
Network Behavior ◽  
Performance Accuracy ◽  
Traffic Generator ◽  
Multiple Devices ◽  
Iot Devices ◽  
The Internet Of Things

We now use the Internet of things (IoT) in our everyday lives. The novel IoT devices collect cyber–physical data and provide information on the environment. Hence, IoT traffic will count for a major part of Internet traffic; however, its impact on the network is still widely unknown. IoT devices are prone to cyberattacks because of constrained resources or misconfigurations. It is essential to characterize IoT traffic and identify each device to monitor the IoT network and discriminate among legitimate and anomalous IoT traffic. In this study, we deployed a smart-home testbed comprising several IoT devices to study IoT traffic. We performed extensive measurement experiments using a novel IoT traffic generator tool called IoTTGen. This tool can generate traffic from multiple devices, emulating large-scale scenarios with different devices under different network conditions. We analyzed the IoT traffic properties by computing the entropy value of traffic parameters and visually observing the traffic on behavior shape graphs. We propose a new method for identifying traffic entropy-based devices, computing the entropy values of traffic features. The method relies on machine learning to classify the traffic. The proposed method succeeded in identifying devices with a performance accuracy up to 94% and is robust with unpredictable network behavior with traffic anomalies spreading in the network.

scholarly journals Multi-Objective Optimization of Integrated Civilian-Military Scheduling of Medical Supplies for Epidemic Prevention and Control

Healthcare ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 126
Author(s):  
Hai-Feng Ling ◽  
Zheng-Lian Su ◽  
Xun-Lin Jiang ◽  
Yu-Jun Zheng
Keyword(s):  
Prevention And Control ◽  
Large Scale ◽  
Medical Services ◽  
The Novel ◽  
Multi Objective ◽  
Medical Supplies ◽  
Problem Instances ◽  
Novel Coronavirus ◽  
And Control ◽  
Minimum Ratio

In a large-scale epidemic, such as the novel coronavirus pneumonia (COVID-19), there is huge demand for a variety of medical supplies, such as medical masks, ventilators, and sickbeds. Resources from civilian medical services are often not sufficient for fully satisfying all of these demands. Resources from military medical services, which are normally reserved for military use, can be an effective supplement to these demands. In this paper, we formulate a problem of integrated civilian-military scheduling of medical supplies for epidemic prevention and control, the aim of which is to simultaneously maximize the overall satisfaction rate of the medical supplies and minimize the total scheduling cost, while keeping a minimum ratio of medical supplies reservation for military use. We propose a multi-objective water wave optimization (WWO) algorithm in order to efficiently solve this problem. Computational results on a set of problem instances constructed based on real COVID-19 data demonstrate the effectiveness of the proposed method.

scholarly journals Comparative genomics suggests a taxonomic revision of the Staphylococcus cohnii species complex

2021 ◽  
Author(s):  
Anna Lavecchia ◽  
Matteo Chiara ◽  
Caterina De Virgilio ◽  
Caterina Manzari ◽  
Carlo Pazzani ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Species Complex ◽  
Large Scale ◽  
Genomic Sequence ◽  
Bacterial Species ◽  
Taxonomic Revision ◽  
Distinct Species ◽  
The Novel ◽  
Staphylococcus Cohnii ◽  
Taxonomic Assignments

Abstract Staphylococcus cohnii (SC), a coagulase-negative bacterium, was first isolated in 1975 from human skin. Early phenotypic analyses led to the delineation of two subspecies (subsp.), Staphylococcus cohnii subsp. cohnii (SCC) and Staphylococcus cohnii subsp. urealyticus (SCU). SCC was considered to be specific to humans whereas SCU apparently demonstrated a wider host range, from lower primates to humans. The type strains ATCC 29974 and ATCC 49330 have been designated for SCC and SCU, respectively. Comparative analysis of 66 complete genome sequences—including a novel SC isolate—revealed unexpected patterns within the SC complex, both in terms of genomic sequence identity and gene content, highlighting the presence of 3 phylogenetically distinct groups. Based on our observations, and on the current guidelines for taxonomic classification for bacterial species, we propose a revision of the SC species complex. We suggest that SCC and SCU should be regarded as two distinct species: SC and SU (Staphylococcus urealyticus), and that two distinct subspecies, SCC and SCB (SC subsp. barensis, represented by the novel strain isolated in Bari) should be recognized within SC. Furthermore, since large scale comparative genomics studies recurrently suggest inconsistencies or conflicts in taxonomic assignments of bacterial species, we believe that the approach proposed here might be considered for more general application.

scholarly journals Scaffolding proteins guide the evolution of algal light harvesting antennas

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Harry W. Rathbone ◽  
Katharine A. Michie ◽  
Michael J. Landsberg ◽  
Beverley R. Green ◽  
Paul M. G. Curmi
Keyword(s):  
Hydrophobic Surface ◽  
Scaffolding Protein ◽  
Secondary Endosymbiosis ◽  
Scaffolding Proteins ◽  
Α Subunit ◽  
Binding Partner ◽  
Photosynthetic Organisms ◽  
New Family ◽  
Red Algal ◽  
Multiple Copies

AbstractPhotosynthetic organisms have developed diverse antennas composed of chromophorylated proteins to increase photon capture. Cryptophyte algae acquired their photosynthetic organelles (plastids) from a red alga by secondary endosymbiosis. Cryptophytes lost the primary red algal antenna, the red algal phycobilisome, replacing it with a unique antenna composed of αβ protomers, where the β subunit originates from the red algal phycobilisome. The origin of the cryptophyte antenna, particularly the unique α subunit, is unknown. Here we show that the cryptophyte antenna evolved from a complex between a red algal scaffolding protein and phycoerythrin β. Published cryo-EM maps for two red algal phycobilisomes contain clusters of unmodelled density homologous to the cryptophyte-αβ protomer. We modelled these densities, identifying a new family of scaffolding proteins related to red algal phycobilisome linker proteins that possess multiple copies of a cryptophyte-α-like domain. These domains bind to, and stabilise, a conserved hydrophobic surface on phycoerythrin β, which is the same binding site for its primary partner in the red algal phycobilisome, phycoerythrin α. We propose that after endosymbiosis these scaffolding proteins outcompeted the primary binding partner of phycoerythrin β, resulting in the demise of the red algal phycobilisome and emergence of the cryptophyte antenna.

A multi-objective sparse evolutionary framework for large-scale weapon target assignment based on a reward strategy

2021 ◽  
Vol 40 (5) ◽  
pp. 10043-10061
Author(s):  
Xiaoping Shi ◽  
Shiqi Zou ◽  
Shenmin Song ◽  
Rui Guo
Keyword(s):  
Large Scale ◽  
The Novel ◽  
Genetic Operators ◽  
Multi Objective ◽  
Target Assignment ◽  
Solution Selection ◽  
Battlefield Environment ◽  
Sparse Problems ◽  
Novel Model ◽  
Error Parameter

 The asset-based weapon target assignment (ABWTA) problem is one of the important branches of the weapon target assignment (WTA) problem. Due to the current large-scale battlefield environment, the ABWTA problem is a multi-objective optimization problem (MOP) with strong constraints, large-scale and sparse properties. The novel model of the ABWTA problem with the operation error parameter is established. An evolutionary algorithm for large-scale sparse problems (SparseEA) is introduced as the main framework for solving large-scale sparse ABWTA problem. The proposed framework (SparseEA-ABWTA) mainly addresses the issue that problem-specific initialization method and genetic operators with a reward strategy can generate solutions efficiently considering the sparsity of variables and an improved non-dominated solution selection method is presented to handle the constraints. Under the premise of constructing large-scale cases by the specific case generator, two numerical experiments on four outstanding multi-objective evolutionary algorithms (MOEAs) show Runtime of SparseEA-ABWTA is faster nearly 50% than others under the same convergence and the gap between MOEAs improved by the mechanism of SparseEA-ABWTA and SparseEA-ABWTA is reduced to nearly 20% in the convergence and distribution.

Derivation of Pheromone-Based Larval Thresholds in Spruce Budworm Accounting for Distance to Defoliated Forest Stands

2021 ◽  
Author(s):  
Marc Rhainds ◽  
Ian DeMerchant ◽  
Pierre Therrien
Keyword(s):  
Boreal Forests ◽  
Large Scale ◽  
Choristoneura Fumiferana ◽  
Intervention Strategy ◽  
Spruce Budworm ◽  
Interactive Effects ◽  
The Novel ◽  
Forest Stands ◽  
General Guideline ◽  
Number Of Males

Abstract Spruce budworm, Choristoneura fumiferana Clem. (Lepidoptera: Tortricidae), is the most severe defoliator of Pinaceae in Nearctic boreal forests. Three tools widely used to guide large-scale management decisions (year-to-year defoliation maps; density of overwintering second instars [L2]; number of males at pheromone traps) were integrated to derive pheromone-based thresholds corresponding to specific intergenerational transitions in larval densities (L2i → L2i+1), taking into account the novel finding that threshold estimates decline with distance to defoliated forest stands (DIST). Estimates of thresholds were highly variable between years, both numerically and in terms of interactive effects of L2i and DIST, which limit their heuristic value. In the context of early intervention strategy (L2i+1 &gt; 6.5 individuals per branch), however, thresholds fluctuated within relatively narrow intervals across wide ranges of L2i and DIST, and values of 40–200 males per trap may thus be used as general guideline.

scholarly journals Comparative Cladistics: Fossils, Morphological Data Partitions and Lost Branches in the Fossil Tree of Life

2017 ◽  
Author(s):  
Ross Mounce
Keyword(s):  
Large Scale ◽  
Phylogenetic Signal ◽  
Scientific Progress ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Sets ◽  
Phylogenetic Groups ◽  
Use Of Data ◽  
Wide Range ◽  
Cladistic Analyses

In this thesis I attempt to gather together a wide range of cladistic analyses of fossil and extant taxa representing a diverse array of phylogenetic groups. I use this data to quantitatively compare the effect of fossil taxa relative to extant taxa in terms of support for relationships, number of most parsimonious trees (MPTs) and leaf stability. In line with previous studies I find that the effects of fossil taxa are seldom different to extant taxa – although I highlight some interesting exceptions. I also use this data to compare the phylogenetic signal within vertebrate morphological data sets, by choosing to compare cranial data to postcranial data. Comparisons between molecular data and morphological data have been previously well explored, as have signals between different molecular loci. But comparative signal within morphological data sets is much less commonly characterized and certainly not across a wide array of clades. With this analysis I show that there are many studies in which the evidence provided by cranial data appears to be be significantly incongruent with the postcranial data – more than one would expect to see just by the effect of chance and noise alone. I devise and implement a modification to a rarely used measure of homoplasy that will hopefully encourage its wider usage. Previously it had some undesirable bias associated with the distribution of missing data in a dataset, but my modification controls for this. I also take an in-depth and extensive review of the ILD test, noting it is often misused or reported poorly, even in recent studies. Finally, in attempting to collect data and metadata on a large scale, I uncovered inefficiencies in the research publication system that obstruct re-use of data and scientific progress. I highlight the importance of replication and reproducibility – even simple reanalysis of high profile papers can turn up some very different results. Data is highly valuable and thus it must be retained and made available for further re-use to maximize the overall return on research investment.

scholarly journals Subanalysis of the AUGUSTUS trial

2020 ◽  
Vol 25 ◽  
pp. 4104
Author(s):  
T. V. Pavlova ◽  
P. D. Duplyakova ◽  
O. V. Shkaeva ◽  
S. P. Krivova
Keyword(s):  
Acute Coronary Syndrome ◽  
Large Scale ◽  
Coronary Intervention ◽  
The Novel ◽  
Actual Clinical Practice ◽  
Coronary Syndrome ◽  
Hospitalization Rates ◽  
Percutaneous Coronary ◽  
Artery Disease ◽  
European Society Of Cardiology

Comorbidity is a common feature of a modern patient. The combination of atrial fibrillation (AF) and various types of coronary artery disease is widespread in actual clinical practice. In such cases, additional pathophysiological mechanisms appear that worsen the clinical course and patient’s prognosis. The management of AF patients who have undergone acute coronary syndrome and/or percutaneous coronary intervention is a challenging problem, which can be solved by large-scale clinical trials. The AUGUSTUS randomized trial with a two-by-two factorial design proved that full-dose apixaban is superior in safety to the vitamin K antagonist warfarin, while not inferior in effectiveness. This pattern has been preserved in several important subanalysis on stent thrombosis, hospitalization rates, and conservative management of acute coronary syndrome. The obtained results are included in the novel European Society of Cardiology guidelines on AF.

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