scholarly journals Conserved Non-exonic Elements: A Novel Class of Marker for Phylogenomics

2016 ◽  
Author(s):  
Scott V. Edwards ◽  
Alison Cloutier ◽  
Allan J. Baker
Keyword(s):  
Gc Content ◽  
Sister Group ◽  
Bootstrap Support ◽  
Phylogenomic Analysis ◽  
Data Set ◽  
The Core ◽  
Phylogenetic Resolution ◽  
New Type ◽  
Flanking Regions

AbstractNoncoding markers have a particular appeal as tools for phylogenomic analysis because, at least in vertebrates, they appear less subject to strong variation in GC content among lineages. Thus far, ultraconserved elements (UCEs) and introns have been the most widely used noncoding markers. Here we analyze and study the evolutionary properties of a new type of noncoding marker, conserved non-exonic elements (CNEEs), which consists of noncoding elements that are estimated to evolve slower than the neutral rate across a set of species. Although they often include UCEs, CNEEs are distinct from UCEs because they are not ultraconserved, and, most importantly, the core region alone is analyzed, rather than both the core and its flanking regions. Using a data set of 16 birds plus an alligator outgroup, and ~3600 - ~3800 loci per marker type, we found that although CNEEs were less variable than UCEs or introns and in some cases exhibited a slower approach to branch resolution as determined by phylogenomic subsampling, the quality of CNEE alignments was superior to those of the other markers, with fewer gaps and missing species. Phylogenetic resolution using coalescent approaches was comparable among the three marker types, with most nodes being fully and congruently resolved. Comparison of phylogenetic results across the three marker types indicated that one branch, the sister group to the passerine+falcon clade, was resolved differently and with moderate (> 70%) bootstrap support between CNEEs and UCEs or introns. Overall, CNEEs appear to be promising as phylogenomic markers, yielding phylogenetic resolution as high as for UCEs and introns but with fewer gaps, less ambiguity in alignments and with patterns of nucleotide substitution more consistent with the assumptions of commonly used methods of phylogenetic analysis.

The Design of Home Intelligent Power Node Based on ZigBee

2015 ◽  
Vol 719-720 ◽  
pp. 561-566
Author(s):  
Yong Qing Gao ◽  
Dan Shanng
Keyword(s):  
Network Node ◽  
Power Parameter ◽  
Home Gateway ◽  
The Core ◽  
Intelligent Home ◽  
Overload Protection ◽  
Zigbee Protocol ◽  
New Type ◽  
Parameter Monitoring

Firstly, this paper analyzes the significance and demand of intelligent power. Then a solution of home intelligent power system based on ZigBee is proposed. Hardware components of the solution proposed in this work mainly consists of AT91SAM9G20 as the core of the home gateway controller, CC430F6137 as the core of the network node of intelligent power and construction of intelligent home network system. This paper mainly introduces a new type of home intelligent power consumption network node, which realizes the measurement of electric power parameter, monitoring, overload protection and timing control, the communication between home gateway and network node through ZigBee protocol, the intelligent household electricity. By testing and using, it can meet the aspects of everyday life needs of user in convenient life, intelligent life and energy-saving, etc. It brings great commercial return and technical value to the development and application of intelligent home in future, as well as far-reaching impact to improving the quality of intelligent home services.

scholarly journals On self-neglect and safeguarding adult reviews: diminishing returns or adding value?

2017 ◽  
Vol 19 (2) ◽  
pp. 53-66 ◽  
Author(s):  
Michael Preston-Shoot
Keyword(s):  
Thematic Analysis ◽  
Annual Reports ◽  
National Database ◽  
Service Improvement ◽  
Policy And Practice ◽  
Data Set ◽  
Content Type ◽  
Core Data ◽  
The Core

Purpose The purpose of this paper is twofold: first, to update the core data set of self-neglect serious case reviews (SCRs) and safeguarding adult reviews (SARs), and accompanying thematic analysis; second, to respond to the critique in the Wood Report of SCRs commissioned by Local Safeguarding Children Boards (LSCBs) by exploring the degree to which the reviews scrutinised here can transform and improve the quality of adult safeguarding practice. Design/methodology/approach Further published reviews are added to the core data set from the websites of Safeguarding Adults Boards (SABs) and from contacts with SAB independent chairs and business managers. Thematic analysis is updated using the four domains employed previously. The findings are then further used to respond to the critique in the Wood Report of SCRs commissioned by LSCBs, with implications discussed for Safeguarding Adult Boards. Findings Thematic analysis within and recommendations from reviews have tended to focus on the micro context, namely, what takes place between individual practitioners, their teams and adults who self-neglect. This level of analysis enables an understanding of local geography. However, there are other wider systems that impact on and influence this work. If review findings and recommendations are to fully answer the question “why”, systemic analysis should appreciate the influence of national geography. Review findings and recommendations may also be used to contest the critique of reviews, namely, that they fail to engage practitioners, are insufficiently systemic and of variable quality, and generate repetitive findings from which lessons are not learned. Research limitations/implications There is still no national database of reviews commissioned by SABs so the data set reported here might be incomplete. The Care Act 2014 does not require publication of reports but only a summary of findings and recommendations in SAB annual reports. This makes learning for service improvement challenging. Reading the reviews reported here against the strands in the critique of SCRs enables conclusions to be reached about their potential to transform adult safeguarding policy and practice. Practical implications Answering the question “why” is a significant challenge for SARs. Different approaches have been recommended, some rooted in systems theory. The critique of SCRs challenges those now engaged in SARs to reflect on how transformational change can be achieved to improve the quality of adult safeguarding policy and practice. Originality/value The paper extends the thematic analysis of available reviews that focus on work with adults who self-neglect, further building on the evidence base for practice. The paper also contributes new perspectives to the process of conducting SARs by using the analysis of themes and recommendations within this data set to evaluate the critique that reviews are insufficiently systemic, fail to engage those involved in reviewed cases and in their repetitive conclusions demonstrate that lessons are not being learned.

scholarly journals Probing core overshooting using subgiant asteroseismology: The case of KIC10273246

2021 ◽  
Vol 647 ◽  
pp. A187
Author(s):  
A. Noll ◽  
S. Deheuvels ◽  
J. Ballot
Keyword(s):  
Stellar Evolution ◽  
Main Sequence ◽  
Seismic Modeling ◽  
General Study ◽  
Data Set ◽  
The Core ◽  
Stellar Ages ◽  
Oscillation Modes ◽  
Mixed Modes

Context. The size of convective cores remains uncertain, despite their substantial influence on stellar evolution, and thus on stellar ages. The seismic modeling of young subgiants can be used to obtain indirect constraints on the core structure during main sequence, thanks to the high probing potential of mixed modes. Aims. We selected the young subgiant KIC10273246, observed by Kepler, based on its mixed-mode properties. We thoroughly modeled this star, with the aim of placing constraints on the size of its main-sequence convective core. A corollary goal of this study is to elaborate a modeling technique that is suitable for subgiants and can later be applied to a larger number of targets. Methods. We first extracted the parameters of the oscillation modes of the star using the full Kepler data set. To overcome the challenges posed by the seismic modeling of subgiants, we propose a method that is specifically tailored to subgiants with mixed modes and uses nested optimization. We then applied this method to perform a detailed seismic modeling of KIC10273246. Results. We obtain models that show good statistical agreements with the observations, both seismic and non-seismic. We show that including core overshooting in the models significantly improves the quality of the seismic fit, optimal models being found for αov = 0.15. Higher amounts of core overshooting strongly worsen the agreement with the observations and are thus firmly ruled out. We also find that having access to two g-dominated mixed modes in young subgiants allows us to place stronger constraints on the gradient of molecular weight in the core and on the central density. Conclusions. This study confirms the high potential of young subgiants with mixed modes to investigate the size of main-sequence convective cores. It paves the way for a more general study including the subgiants observed with Kepler, TESS, and eventually PLATO.

scholarly journals Corrigendum to: Phylogeny and biogeography of the ant subfamily Myrmeciinae (Hymenoptera : Formicidae)

2003 ◽  
Vol 17 (4) ◽  
pp. 605 ◽  
Author(s):  
Philip S. Ward ◽  
Seán G. Brady
Keyword(s):  
Sequence Data ◽  
Strong Support ◽  
Sister Group ◽  
Molecular Data ◽  
Morphological Data ◽  
Recent Common Ancestor ◽  
Bootstrap Support ◽  
Data Set ◽  
Molecular Sequence Data ◽  
Most Recent Common Ancestor

We investigated phylogenetic relationships among the 'primitive' Australian ant genera Myrmecia and Nothomyrmecia (stat. rev.) and the Baltic amber fossil genus Prionomyrmex, using a combination of morphological and molecular data. Outgroups for the analysis included representatives from a variety of potential sister-groups, including five extant subfamilies of ants and one extinct group (Sphecomyrminae). Parsimony analysis of the morphological data provides strong support (~95% bootstrap proportions) for the monophyly of (1) genus Myrmecia, (2) genus Prionomyrmex, and (3) a clade containing those two genera plus Nothomyrmecia. A group comprising Nothomyrmecia and Prionomyrmex is also upheld (85% bootstrap support). Molecular sequence data (~2200 base pairs from the 18S and 28S ribosomal RNA genes) corroborate these findings for extant taxa, with Myrmecia and Nothomyrmecia appearing as sister-groups with ~100% bootstrap support under parsimony, neighbour-joining and maximum-likelihood analyses. Neither the molecular nor the morphological data set allows us to identify unambiguously the sister-group of (Myrmecia + (Nothomyrmecia + Prionomyrmex)). Rather, Myrmecia and relatives are part of an unresolved polytomy that encompasses most of the ant subfamilies. Taken as a whole, our results support the contention that many of the major lineages of ants – including a clade that later came to contain Myrmecia, Nothomyrmecia and Prionomyrmex – arose at around the same time during a bout of diversification in the middle or late Cretaceous. On the basis of Bayesian dating analysis, the estimated age of the most recent common ancestor of Myrmecia and Nothomyrmecia is 74 million years (95% confidence limits, 53–101�million years), a result consistent with the origin of the myrmeciine stem lineage in the Cretaceous. The ant subfamily Myrmeciinae is redefined to contain two tribes, Myrmeciini (genus Myrmecia) and Prionomyrmecini (Nothomyrmecia and Prionomyrmex). Phylogenetic analysis of the enigmatic Argentine fossils Ameghinoia and Polanskiella demonstrates that they are also members of the Myrmeciinae, probably more closely related to Prionomyrmecini than to Myrmeciini. Thus, the myrmeciine ants appear to be a formerly widespread group that retained many ancestral formicid characteristics and that became extinct everywhere except in the Australian region.

scholarly journals QUALITY ASSESSMENT OF LAND COVER CLASSIFICATION PRODUCTS BASED ON THE FUZZY–AHP SYNTHESIS MODEL

2021 ◽  
Vol XLIII-B3-2021 ◽  
pp. 769-773
Author(s):  
L. Lv ◽  
H. Chen ◽  
W. Xie ◽  
Z. Tian ◽  
Y. Chen
Keyword(s):  
Land Cover ◽  
Fuzzy Ahp ◽  
Weighted Average ◽  
Northern China ◽  
Land Cover Classification ◽  
Data Set ◽  
National Geographic ◽  
Inspection Process ◽  
New Type

Abstract. As one of the critical products National Geographic Conditions Monitoring Achievements (NGCMA), land cover dataset has great value for the practical needs of China natural resources investigation and monitoring. For providing This paper proposed a fuzzy-AHP synthesis model, for assessing the quality of land cover classification products, based on the current qualifications of inspection and acceptance as well the characteristics of the inspection process of this type of results. The model is practiced on a data set that is the inspection results from 27 surveying areas in northern China. By comparing the results to the results from minimum method (MinM) and weighted average methods (WAM), this study pay attention on giving the analysing of the reasonability and feasibility of this model on practical uses and to provide a technical reference for quality evaluation of the new-type of fundamental surveying and mapping products.

scholarly journals The first complete plastid genomes of Melastomataceae are highly structurally conserved

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2715 ◽  
Author(s):  
Marcelo Reginato ◽  
Kurt M. Neubig ◽  
Lucas C. Majure ◽  
Fabian A. Michelangeli
Keyword(s):  
Genomic Structure ◽  
Phylogenetic Analyses ◽  
Gc Content ◽  
Pcr Amplification ◽  
Land Plant ◽  
Small Sample ◽  
Sequence Length ◽  
Bootstrap Support ◽  
Data Set ◽  
Plastid Genomes

BackgroundIn the past three decades, several studies have predominantly relied on a small sample of the plastome to infer deep phylogenetic relationships in the species-rich Melastomataceae. Here, we report the first full plastid sequences of this family, compare general features of the sampled plastomes to other sequenced Myrtales, and survey the plastomes for highly informative regions for phylogenetics.MethodsGenome skimming was performed for 16 species spread across the Melastomataceae. Plastomes were assembled, annotated and compared to eight sequenced plastids in the Myrtales. Phylogenetic inference was performed using Maximum Likelihood on six different data sets, where putative biases were taken into account. Summary statistics were generated for all introns and intergenic spacers with suitable size for polymerase chain reaction (PCR) amplification and used to rank the markers by phylogenetic information.ResultsThe majority of the plastomes sampled are conserved in gene content and order, as well as in sequence length and GC content within plastid regions and sequence classes. Departures include the putative presence ofrps16andrpl2pseudogenes in some plastomes. Phylogenetic analyses of the majority of the schemes analyzed resulted in the same topology with high values of bootstrap support. Although there is still uncertainty in some relationships, in the highest supported topologies only two nodes received bootstrap values lower than 95%.DiscussionMelastomataceae plastomes are no exception for the general patterns observed in the genomic structure of land plant chloroplasts, being highly conserved and structurally similar to most other Myrtales. Despite the fact that the full plastome phylogeny shares most of the clades with the previously widely used and reduced data set, some changes are still observed and bootstrap support is higher. The plastome data set presented here is a step towards phylogenomic analyses in the Melastomataceae and will be a useful resource for future studies.

scholarly journals Spider phylogenomics: untangling the Spider Tree of Life

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1719 ◽  
Author(s):  
Nicole L. Garrison ◽  
Juanita Rodriguez ◽  
Ingi Agnarsson ◽  
Jonathan A. Coddington ◽  
Charles E. Griswold ◽  
...  
Keyword(s):  
Sister Group ◽  
Acid Sites ◽  
Molecular Dating ◽  
Phylogenomic Analysis ◽  
Ancestral State ◽  
Data Set ◽  
Key Innovation ◽  
Orb Web ◽  
Phylogenomic Analyses ◽  
High Level

Spiders (Order Araneae) are massively abundant generalist arthropod predators that are found in nearly every ecosystem on the planet and have persisted for over 380 million years. Spiders have long served as evolutionary models for studying complex mating and web spinning behaviors, key innovation and adaptive radiation hypotheses, and have been inspiration for important theories like sexual selection by female choice. Unfortunately, past major attempts to reconstruct spider phylogeny typically employing the “usual suspect” genes have been unable to produce a well-supported phylogenetic framework for the entire order. To further resolve spider evolutionary relationships we have assembled a transcriptome-based data set comprising 70 ingroup spider taxa. Using maximum likelihood and shortcut coalescence-based approaches, we analyze eight data sets, the largest of which contains 3,398 gene regions and 696,652 amino acid sites forming the largest phylogenomic analysis of spider relationships produced to date. Contrary to long held beliefs that the orb web is the crowning achievement of spider evolution, ancestral state reconstructions of web type support a phylogenetically ancient origin of the orb web, and diversification analyses show that the mostly ground-dwelling, web-less RTA clade diversified faster than orb weavers. Consistent with molecular dating estimates we report herein, this may reflect a major increase in biomass of non-flying insects during the Cretaceous Terrestrial Revolution 125–90 million years ago favoring diversification of spiders that feed on cursorial rather than flying prey. Our results also have major implications for our understanding of spider systematics. Phylogenomic analyses corroborate several well-accepted high level groupings: Opisthothele, Mygalomorphae, Atypoidina, Avicularoidea, Theraphosoidina, Araneomorphae, Entelegynae, Araneoidea, the RTA clade, Dionycha and the Lycosoidea. Alternatively, our results challenge the monophyly of Eresoidea, Orbiculariae, and Deinopoidea. The composition of the major paleocribellate and neocribellate clades, the basal divisions of Araneomorphae, appear to be falsified. Traditional Haplogynae is in need of revision, as our findings appear to support the newly conceived concept of Synspermiata. The sister pairing of filistatids with hypochilids implies that some peculiar features of each family may in fact be synapomorphic for the pair. Leptonetids now are seen as a possible sister group to the Entelegynae, illustrating possible intermediates in the evolution of the more complex entelegyne genitalic condition, spinning organs and respiratory organs.

Data Exploration by Representative Region Selection: Axioms and Convergence

2021 ◽  
Author(s):  
Alexander S. Estes ◽  
Michael O. Ball ◽  
David J. Lovell
Keyword(s):  
Optimization Problems ◽  
Cluster Structure ◽  
Data Set ◽  
Quality Function ◽  
Additional Information ◽  
Region Selection ◽  
Convergence Results ◽  
Small Set ◽  
New Type

We present a new type of unsupervised learning problem in which we find a small set of representative regions that approximates a larger data set. These regions may be presented to a practitioner along with additional information in order to help the practitioner explore the data set. An advantage of this approach is that it does not rely on cluster structure of the data. We formally define this problem, and we present axioms that should be satisfied by functions that measure the quality of representatives. We provide a quality function that satisfies all of these axioms. Using this quality function, we formulate two optimization problems for finding representatives. We provide convergence results for a general class of methods, and we show that these results apply to several specific methods, including methods derived from the solution of the optimization problems formulated in this paper. We provide an example of how representative regions may be used to explore a data set.

scholarly journals Genome of Superficieibacter maynardsmithii, a novel, antibiotic susceptible representative of Enterobacteriaceae

2021 ◽  
Vol 11 (2) ◽  
Author(s):  
Gherard Batisti Biffignandi ◽  
Marjorie J Gibbon ◽  
Marta Corbella ◽  
Harry A Thorpe ◽  
Cristina Merla ◽  
...  
Keyword(s):  
New Species ◽  
Draft Genome ◽  
Gc Content ◽  
Sister Group ◽  
Sister Group Relationship ◽  
Phylogenomic Analysis ◽  
The Novel ◽  
Antimicrobial Resistance Genes ◽  
The Family ◽  
A New Species

Abstract During a citywide microbiological screening project in Pavia (Italy) a bacterial strain isolated from the surface of an Automated Teller Machine was classified as a Klebsiella sp. by MALDI-TOF spectrometry, and shown to be susceptible to the most antimicrobial classes by phenotypic testing. After Illumina genome sequencing and subsequent assembly, a high-quality draft genome was obtained (size = 5,051,593 bp, N50 = 615,571 bp, largest contig = 1,328,029 bp, N_contig = 17, GC content = 51.58%, coverage = 141.42), absence of antimicrobial resistance genes was confirmed, but the strain resulted to be highly divergent from all Klebsiella, and more related to other Enterobacteriaceae. The higher values of 16S rRNA identity were with members of the genera Citrobacter, Salmonella, and “Superficieibacter.” An ortholog-based phylogenomic analysis indicated a sister group relationship with “Superficieibacter electus,” in a distinct clade from other members of the Enterobacteriaceae family. In order to evaluate whether the novel genome represents a new species of “Superficiebacter,” average nucleotide identity (ANI) and Hadamard analysis were performed on a dataset of 78 Enterobacteriaceae. The novel genome showed an ANI of 87.51% with S. electus, which compared on identity values between other members of the family, clearly indicates that the genome represents a new species within the genus “Superficieibacter.” We propose for the new species the name “Superficieibacter maynardsmithii.”

scholarly journals Peer-Reviewed Open Research Data: Results of a Pilot

2012 ◽  
Vol 7 (2) ◽  
pp. 81-91 ◽  
Author(s):  
Marjan Grootveld ◽  
Jeff Van Egmond
Keyword(s):  
Pilot Study ◽  
Peer Review ◽  
Research Data ◽  
Research Quality ◽  
Data Sets ◽  
Electronic Archive ◽  
Data Set ◽  
The Core ◽  
Open Research

Peer review of publications is at the core of science and primarily seen as instrument for ensuring research quality. However, it is less common to independently value the quality of the underlying data as well. In the light of the ‘data deluge’ it makes sense to extend peer review to the data itself and this way evaluate the degree to which the data are fit for re-use. This paper describes a pilot study at EASY - the electronic archive for (open) research data at our institution. In EASY, researchers can archive their data and add metadata themselves. Devoted to open access and data sharing, at the archive we are interested in further enriching these metadata with peer reviews.As a pilot, we established a workflow where researchers who have downloaded data sets from the archive were asked to review the downloaded data set. This paper describes the details of the pilot including the findings, both quantitative and qualitative. Finally, we discuss issues that need to be solved when such a pilot is turned into a structural peer review functionality for the archiving system.

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