Impact of the choices of calibration points for molecular dating: a case study of Ensifera

2021 ◽  
Vol 4 (3) ◽  
Author(s):  
ANDRÉ NEL
Keyword(s):  
Molecular Dating ◽  
Rigorous Approach ◽  
Phylogenetic Studies

Fossils are crucial for molecular clade dating (Warnock et al., 2012, 2015). But it is necessary to have a rigorous approach, without rejecting taxa on poor arguments or ignoring some of them without any reasons. Here we show through two very recent examples of phylogenetic studies on the Orthoptera, that such behaviours can have dramatic consequences on the value of the results of the studies.

scholarly journals Pathologic validation of an yttrium-90 trans-arterial radioembolization dosimetry: a case report

2021 ◽  
Vol 2021 (4) ◽  
Author(s):  
Jacqueline B Baikovitz ◽  
Lindsay Thornton ◽  
Monica T Garcia-Buitrago ◽  
Alan S Livingstone ◽  
Matthew T Studenski ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Case Report ◽  
Liver Resection ◽  
Pathologic Response ◽  
Clinical Scenario ◽  
Complete Pathologic Response ◽  
Pathological Findings ◽  
Rigorous Approach ◽  
Yttrium 90

Abstract Yttrium-90 (Y-90) trans-arterial radioembolization (TARE) is used in the management of unresectable hepatocellular carcinoma (HCC). During the last 5 years, dosimetry software has been developed to allow for a more rigorous approach of dose prescription in Y-90 TARE. We present here a case study of a 77-year-old woman diagnosed with HCC, who underwent a Y-90 TARE as a bridge procedure to liver resection. This clinical scenario represents a unique opportunity to illustrate the predictive value of dosimetric findings correlating dosimetry with pathological findings. In this case, Y-90 TARE dosimetry was predictive of treatment response in which the tumor received a mean dose of 156 Gy and demonstrated a complete pathologic response.

A critical analysis of water PPP failures in sub-Saharan Africa

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Salman Tariq ◽  
Xueqing Zhang
Keyword(s):  
Construction Management ◽  
Design Methodology ◽  
Sub Saharan Africa ◽  
African Countries ◽  
Content Type ◽  
Rigorous Approach ◽  
First Case ◽  
Management Perspective ◽  
Sub Saharan

PurposeTop-down pressure from donors, public sector inefficiencies and fund deficits have steered the introduction of public–private partnerships (PPPs) in sub-Saharan Africa. However, PPP activities in the water sector have been quite insignificant compared to other infrastructure sectors in this region. In addition, a number of water PPPs have encountered great difficulties and subsequent failures. This study aims at unveiling the underlying reasons behind failures.Design/methodology/approachThis study has classified the failure types of water PPPs and reviewed the development of water PPPs in sub-Saharan Africa to identify failed ones. Eight failed case studies are completed through the rigorous approach of event sequence mapping.FindingsNine root causes of water PPP failure are identified through a thorough examination of these failed water PPP cases and the interrelationships between these failure causes are established. The failure causes are further generalized through literature focusing on water PPP failures in developing countries and problematic issues that hinder the implementation of successful water PPPs across different Sub-Saharan African countries. Recommendations are provided for future improvements in carrying out water PPPs in Sub-Saharan Africa by learning past lessons and drawing experiences.Originality/valueThis is the first case study on water PPP failures in Sub-Saharan Africa from a construction management perspective. This study will help governments and the private sector in developing stronger future water PPPs.

scholarly journals THE VALIDATION OF THE TRANSFORMATION BETWEEN AN OLD GEODETIC REFERENCE FRAME AND A MODERN REFERENCE FRAME, BY USING EXTERNAL SPACE TECHNIQUES SITES: THE CASE STUDY OF THE HELLENIC GEODETIC REFERENCE SYSTEM OF 1987

2017 ◽  
Vol 23 (3) ◽  
pp. 434-444 ◽  
Author(s):  
Ioannis D. Doukas ◽  
Dimitrios Ampatzidis ◽  
Vassileios Kampouris
Keyword(s):  
Reference Frame ◽  
Reference Frames ◽  
Dynamic Change ◽  
Geodetic Reference System ◽  
Bias Estimation ◽  
Rigorous Approach ◽  
Systematic Effects ◽  
Tectonic Motion ◽  
Geodetic Reference Frame

Abstract: Many of the old geodetic reference frames which realized in the previous decades using classical observations carry biases. These biases are mainly caused due to the problematic observations and/or the tectonic motion. That is the case of the official Greek geodetic reference frame which consists of classical and satellite observations. Herein, we present a rigorous approach of the reconstruction of the Greek official reference frame based on the modern geodetic reference frames and their ability to express the spatial position and the dynamic change of the stations. We applied the rigorous approach to ninety stations located in Greece and we compare it with the officially accepted procedure. We found a consistency at 59.4cm between the rigorous and the officially accepted approaches, respectively. The associated mean bias estimation was estimated at 51.4 cm, indicating the resistance of a rather large amount of systematic effects. In addition, the observed discrepancies between the two approaches show great inhomogeneity all over the country.

scholarly journals A protocol for retrospective translational science case studies of health interventions

2020 ◽  
pp. 1-7
Author(s):  
Sara E. Dodson ◽  
Ira Kukic ◽  
Linda Scholl ◽  
Clara M. Pelfrey ◽  
William M. Trochim
Keyword(s):  
Case Studies ◽  
Research Process ◽  
Health Interventions ◽  
Research Translation ◽  
Translational Science ◽  
Key Factors ◽  
Rigorous Approach ◽  
Study Approach

Abstract The critical processes driving successful research translation remain understudied. We describe a mixed-method case study protocol for analyzing translational research that has led to the successful development and implementation of innovative health interventions. An overarching goal of these case studies is to describe systematically the chain of events between basic, fundamental scientific discoveries and the adoption of evidence-based health applications, including description of varied, long-term impacts. The case study approach isolates many of the key factors that enable the successful translation of research into practice and provides compelling evidence connecting the intervention to measurable changes in health and medical practice, public health outcomes, and other broader societal impacts. The goal of disseminating this protocol is to systematize a rigorous approach, which can enhance reproducibility, promote the development of a large collection of comparable studies, and enable cross-case analyses. This approach, an application of the “science of translational science,” will lead to a better understanding of key research process markers, timelines, and potential points of leverage for intervention that may help facilitate decisions, processes, and policies to speed the sustainable translational process. Case studies are effective communication vehicles to demonstrate both accountability and the impacts of the public’s investment in research.

The importance of molecular dating analyses for inferring Hawaiian biogeographical history: a case study with bark lice (Psocidae:Ptycta)

2013 ◽  
Vol 41 (1) ◽  
pp. 158-167 ◽  
Author(s):  
Emilie C. Bess ◽  
Therese A. Catanach ◽  
Kevin P. Johnson
Keyword(s):  
Molecular Dating ◽  
Bark Lice

scholarly journals Mitogenomics and mitochondrial gene phylogeny decipher the evolution of Saccharomycotina yeasts

2021 ◽  
Author(s):  
Anastasia C Christinaki ◽  
Spyros G Kanellopoulos ◽  
Alexandra M Kortsinoglou ◽  
Bart Theelen ◽  
Teun Boekhout ◽  
...  
Keyword(s):  
Genetic Code ◽  
Genome Size ◽  
Genetic Recombination ◽  
Mitochondrial Gene ◽  
Molecular Dating ◽  
Phylogenetic Studies ◽  
Intergenic Regions ◽  
Size Diversity ◽  
Phylogenetic Lineages ◽  
Mt Genome

Saccharomycotina yeasts contain diverse clades within the kingdom of Fungi and are important to human everyday life. This work investigates the evolutionary relationships among these yeasts from a mitochondrial (mt) genomic perspective. A comparative study of 141 yeast mt genomes representing all major phylogenetic lineages of Saccharomycotina was performed, including genome size and content variability, intron and intergenic regions' diversity, genetic code alterations and syntenic variation. Findings from this study suggest that mt genome size diversity is the result of a ceaseless random process mainly based on genetic recombination and intron mobility. Gene order analysis revealed conserved syntenic units and many occurring rearrangements, which can be correlated with major evolutionary events as shown by the phylogenetic analysis of the concatenated mt protein matrix. For the first time, molecular dating indicated a slower mt genome divergence rate in the early stages of yeast evolution, in contrast with a faster rate in the late evolutionary stages, compared to their nuclear time divergence. Genetic code reassignments of mt genomes are a perpetual process happening in many different parallel evolutionary steps throughout Saccharomycotina evolution. Overall, this work shows that phylogenetic studies that employ the mt genome of yeasts highlight major evolutionary events.

scholarly journals Datataxa: a new script to extract metadata sequence information from GenBank, the Flora of Bajío as a case study

2019 ◽  
Vol 97 (4) ◽  
pp. 754-760
Author(s):  
Eduardo Ruiz-Sanchez ◽  
Carlos Alonso Maya-Lastra ◽  
Victor W. Steinmann ◽  
Sergio Zamudio ◽  
Eleazar Carranza ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sequence Information ◽  
Public Repository ◽  
Phylogenetic Studies ◽  
Meta Information ◽  
Study Case ◽  
Scripting Language ◽  
Diversity Studies ◽  
Extract Information

Background: GenBank is a public repository that houses millions of nucleotide sequences. Several software have been developed to extract information stored in GenBank. However, none of them are useful to extract and organize GenBank accession based on metadata. We developed a new script called Datataxa, which works to mine GenBank information. The checklist of the Flora del Bajío y de Regiones Adyacentes (FBRA) was used as a case study to apply our script.Questions: How many species occurring in the FBRA have records in GenBank? What percentage of those records have been used for phylogenetic, phylogeographic, phylogenomic, barcoding, genetic diversity, and biogeographic studies?Methods: Datataxa was written in AutoIt Scripting Language in order to facilitate the extraction of information from GenBank. This information was classified in six study categories. A checklist of species published fascicles of FBRA was used as study case to apply our new script, and the previous categories were applied to the FBRA species list.Results: The script allowed us to search for meta information, like publication titles, for 2,558 species that were included in the FBRA. Of these, 1,575 had a least one record in GenBank. A total of 1,322 species were used in phylogenetic studies, followed by barcoding studies (326) and biogeographic studies (298). Phylogenomic (41), phylogeographic (34), and diversity studies (34) were the least represented.Conclusions: Datataxa was useful for mining metadata sequence information from GenBank and can be used with any list of species to get the GenBank accessions’ metadata.

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