scholarly journals European phylogeography of Rhyacophila tristis Pictet (Trichoptera: Rhyacophilidae): preliminary results

Zoosymposia ◽  
2011 ◽  
Vol 5 (1) ◽  
pp. 11-18 ◽  
Author(s):  
MIKLÓS BÁLINT ◽  
LUJZA UJVÁROSI ◽  
A. LEHEL DÉNES ◽  
OCTAVIAN POPESCU
Keyword(s):  
Large Scale ◽  
Sequence Data ◽  
Wide Spread ◽  
Central European ◽  
Preliminary Results ◽  
Phylogeographic Analysis ◽  
Genetic Patterns ◽  
Scale Population ◽  
The Alps ◽  
Study Species

We present preliminary results of a phylogeographic analysis of Rhyacophila tristis, a wide-spread European caddisfly. Mitochondrial sequence data (the second part of the mtCOI gene) of 52 of specimens were used to investigate large-scale population genetic patterns of Central European populations of the study species. The results show strong genetic differences between a western and an eastern lineage. The deep split most probably indicates that the identified lineages of R. tristis survived in independent Pleistocene refugia in the Alps and in the Carpathians, emphasizing the importance of these areas in the Pleistocene survival of aquatic mountain organisms

scholarly journals Large scale population screening for Duchenne muscular dystrophy – Preliminary results

2022 ◽  
Vol 226 (1) ◽  
pp. S347
Author(s):  
Gal Cohen ◽  
Atalia Shtorch-Asor ◽  
Racheli Goldfarb-Yaacobi ◽  
Meirav Kaiser ◽  
Revital Rosenfeld ◽  
...  
Keyword(s):  
Duchenne Muscular Dystrophy ◽  
Muscular Dystrophy ◽  
Large Scale ◽  
Population Screening ◽  
Preliminary Results ◽  
Scale Population

scholarly journals Ancestrally and Temporally Diverse Analysis of Penetrance of Clinical Variants in 72,434 Individuals

2021 ◽  
Author(s):  
Iain S. Forrest ◽  
Kumardeep Chaudhary ◽  
Ha My T. Vy ◽  
Shantanu Bafna ◽  
Daniel M. Jordan ◽  
...  
Keyword(s):  
Large Scale ◽  
Disease Risk ◽  
Sequence Data ◽  
Genomic Medicine ◽  
Population Based ◽  
Loss Of Function ◽  
Pathogenic Variants ◽  
Scale Population ◽  
Predisposition Genes ◽  
Disease Predisposition

ABSTRACTA major goal of genomic medicine is to quantify the disease risk of genetic variants. Here, we report the penetrance of 37,772 clinically relevant variants (including those reported in ClinVar1 and of loss-of-function consequence) for 197 diseases in an analysis of exome sequence data for 72,434 individuals over five ancestries and six decades of ages from two large-scale population-based biobanks (BioMe Biobank and UK Biobank). With a high-quality set of 5,359 clinically impactful variants, we evaluate disease prevalence in carriers and non-carriers to interrogate major determinants and implications of penetrance. First, we associate biomarker levels with penetrance of variants in known disease-predisposition genes and illustrate their clear biological link to disease. We then systematically uncover large numbers of ClinVar pathogenic variants that confer low risk of disease, even among those reviewed by experts, while delineating stark differences in variant penetrance by molecular consequence. Furthermore, we ascertain numerous variants present in non-European ancestries and reveal how increasing carrier age modifies penetrance estimates. Lastly, we examine substantial heterogeneity of penetrance among variants in known disease-predisposition genes for conditions such as familial hypercholesterolemia and breast cancer. These data indicate that existing categorical systems for variant classification do not adequately capture disease risk and warrant consideration of a more quantitative system based on population-based penetrance to evaluate clinical impact.

Preliminary results from follow-up of a large-scale population survey of antibodies to gliadin, reticulin and endomysium

1996 ◽  
Vol 85 (s412) ◽  
pp. 61-64 ◽  
Author(s):  
SD Johnston ◽  
RGP Watson ◽  
SA McMillan ◽  
D McMaster ◽  
A Evans
Keyword(s):  
Large Scale ◽  
Population Survey ◽  
Preliminary Results ◽  
Scale Population

scholarly journals Dynamic Planning of Bicycle Stations in Dockless Public Bicycle-sharing System Using Gated Graph Neural Network

2021 ◽  
Vol 12 (2) ◽  
pp. 1-22
Author(s):  
Jianguo Chen ◽  
Kenli Li ◽  
Keqin Li ◽  
Philip S. Yu ◽  
Zeng Zeng
Keyword(s):  
Large Scale ◽  
Sequence Data ◽  
Location Prediction ◽  
City Management ◽  
Dynamic Planning ◽  
Graph Sequence ◽  
Graph Modeling ◽  
The Government ◽  
Location Clustering ◽  
Station Location

Benefiting from convenient cycling and flexible parking locations, the Dockless Public Bicycle-sharing (DL-PBS) network becomes increasingly popular in many countries. However, redundant and low-utility stations waste public urban space and maintenance costs of DL-PBS vendors. In this article, we propose a Bicycle Station Dynamic Planning (BSDP) system to dynamically provide the optimal bicycle station layout for the DL-PBS network. The BSDP system contains four modules: bicycle drop-off location clustering, bicycle-station graph modeling, bicycle-station location prediction, and bicycle-station layout recommendation. In the bicycle drop-off location clustering module, candidate bicycle stations are clustered from each spatio-temporal subset of the large-scale cycling trajectory records. In the bicycle-station graph modeling module, a weighted digraph model is built based on the clustering results and inferior stations with low station revenue and utility are filtered. Then, graph models across time periods are combined to create a graph sequence model. In the bicycle-station location prediction module, the GGNN model is used to train the graph sequence data and dynamically predict bicycle stations in the next period. In the bicycle-station layout recommendation module, the predicted bicycle stations are fine-tuned according to the government urban management plan, which ensures that the recommended station layout is conducive to city management, vendor revenue, and user convenience. Experiments on actual DL-PBS networks verify the effectiveness, accuracy, and feasibility of the proposed BSDP system.

scholarly journals The Evolution of Life Modes in Stictidaceae, with Three Novel Taxa

2021 ◽  
Vol 7 (2) ◽  
pp. 105
Author(s):  
Vinodhini Thiyagaraja ◽  
Robert Lücking ◽  
Damien Ertz ◽  
Samantha C. Karunarathna ◽  
Dhanushka N. Wanasinghe ◽  
...  
Keyword(s):  
New Species ◽  
Large Scale ◽  
Sequence Data ◽  
Large Subunit ◽  
Monte Carlo Sampling ◽  
Small Subunit ◽  
Sensu Stricto ◽  
Internal Transcribed Spacers ◽  
Character State ◽  
Phenotypic Data

Ostropales sensu lato is a large group comprising both lichenized and non-lichenized fungi, with several lineages expressing optional lichenization where individuals of the same fungal species exhibit either saprotrophic or lichenized lifestyles depending on the substrate (bark or wood). Greatly variable phenotypic characteristics and large-scale phylogenies have led to frequent changes in the taxonomic circumscription of this order. Ostropales sensu lato is currently split into Graphidales, Gyalectales, Odontotrematales, Ostropales sensu stricto, and Thelenellales. Ostropales sensu stricto is now confined to the family Stictidaceae, which includes a large number of species that are poorly known, since they usually have small fruiting bodies that are rarely collected, and thus, their taxonomy remains partly unresolved. Here, we introduce a new genus Ostropomyces to accommodate a novel lineage related to Ostropa, which is composed of two new species, as well as a new species of Sphaeropezia, S. shangrilaensis. Maximum likelihood and Bayesian inference analyses of mitochondrial small subunit spacers (mtSSU), large subunit nuclear rDNA (LSU), and internal transcribed spacers (ITS) sequence data, together with phenotypic data documented by detailed morphological and anatomical analyses, support the taxonomic affinity of the new taxa in Stictidaceae. Ancestral character state analysis did not resolve the ancestral nutritional status of Stictidaceae with confidence using Bayes traits, but a saprotrophic ancestor was indicated as most likely in a Bayesian binary Markov Chain Monte Carlo sampling (MCMC) approach. Frequent switching in nutritional modes between lineages suggests that lifestyle transition played an important role in the evolution of this family.

scholarly journals Publisher Correction: A link between appendectomy and gastrointestinal cancers: a large-scale population-based cohort study in Korea

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Youn Young Park ◽  
Kil‑yong Lee ◽  
Seong Taek Oh ◽  
Sang Hyun Park ◽  
Kyung Do Han ◽  
...  
Keyword(s):  
Cohort Study ◽  
Large Scale ◽  
Population Based ◽  
Gastrointestinal Cancers ◽  
Scale Population

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

scholarly journals Using Bus Ticketing Big Data to Investigate the Behaviors of the Population Flow of Chinese Suburban Residents in the Post-COVID-19 Phase

2021 ◽  
Vol 18 (11) ◽  
pp. 6066
Author(s):  
Yanbing Bai ◽  
Lu Sun ◽  
Haoyu Liu ◽  
Chao Xie
Keyword(s):  
Travel Behavior ◽  
Large Scale ◽  
Behavior Patterns ◽  
Population Movements ◽  
Economic Level ◽  
Passenger Travel ◽  
Scale Population ◽  
Travel Behaviors ◽  
Railway Passenger ◽  
And Control

Large-scale population movements can turn local diseases into widespread epidemics. Grasping the characteristic of the population flow in the context of the COVID-19 is of great significance for providing information to epidemiology and formulating scientific and reasonable prevention and control policies. Especially in the post-COVID-19 phase, it is essential to maintain the achievement of the fight against the epidemic. Previous research focuses on flight and railway passenger travel behavior and patterns, but China also has numerous suburban residents with a not-high economic level; investigating their travel behaviors is significant for national stability. However, estimating the impacts of the COVID-19 for suburban residents’ travel behaviors remains challenging because of lacking apposite data. Here we submit bus ticketing data including approximately 26,000,000 records from April 2020–August 2020 for 2705 stations. Our results indicate that Suburban residents in Chinese Southern regions are more likely to travel by bus, and travel frequency is higher. Associated with the economic level, we find that residents in the economically developed region more likely to travel or carry out various social activities. Considering from the perspective of the traveling crowd, we find that men and young people are easier to travel by bus; however, they are exactly the main workforce. The indication of our findings is that suburban residents’ travel behavior is affected profoundly by economy and consistent with the inherent behavior patterns before the COVID-19 outbreak. We use typical regions as verification and it is indeed the case.

scholarly journals Whole-genome sequence data suggests environmental adaptation of Ethiopian sheep populations

2021 ◽  
Author(s):  
Pamela Wiener ◽  
Christelle Robert ◽  
Abulgasim Ahbara ◽  
Mazdak Salavati ◽  
Ayele Abebe ◽  
...  
Keyword(s):  
High Altitude ◽  
Environmental Variables ◽  
Large Scale ◽  
Sequence Data ◽  
Strong Association ◽  
Environmental Adaptation ◽  
Whole Genome Sequence ◽  
Single Nucleotide Variants ◽  
High Altitude Adaptation ◽  
Altitude Adaptation

Abstract Great progress has been made over recent years in the identification of selection signatures in the genomes of livestock species. This work has primarily been carried out in commercial breeds for which the dominant selection pressures, are associated with artificial selection. As agriculture and food security are likely to be strongly affected by climate change, a better understanding of environment-imposed selection on agricultural species is warranted. Ethiopia is an ideal setting to investigate environmental adaptation in livestock due to its wide variation in geo-climatic characteristics and the extensive genetic and phenotypic variation of its livestock. Here, we identified over three million single nucleotide variants across 12 Ethiopian sheep populations and applied landscape genomics approaches to investigate the association between these variants and environmental variables. Our results suggest that environmental adaptation for precipitation-related variables is stronger than that related to altitude or temperature, consistent with large-scale meta-analyses of selection pressure across species. The set of genes showing association with environmental variables was enriched for genes highly expressed in human blood and nerve tissues. There was also evidence of enrichment for genes associated with high-altitude adaptation although no strong association was identified with hypoxia-inducible-factor (HIF) genes. One of the strongest altitude-related signals was for a collagen gene, consistent with previous studies of high-altitude adaptation. Several altitude-associated genes also showed evidence of adaptation with temperature, suggesting a relationship between responses to these environmental factors. These results provide a foundation to investigate further the effects of climatic variables on small ruminant populations.

scholarly journals A Phylogenomic Supertree of Birds

Diversity ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 109 ◽  
Author(s):  
Rebecca T. Kimball ◽  
Carl H. Oliveros ◽  
Ning Wang ◽  
Noor D. White ◽  
F. Keith Barker ◽  
...  
Keyword(s):  
Large Scale ◽  
Sequence Data ◽  
Bird Species ◽  
Divide And Conquer ◽  
Clear Understanding ◽  
Whole Genome ◽  
Efficient Manner ◽  
Sequence Capture ◽  
Branch Lengths ◽  
Supertree Methods

It has long been appreciated that analyses of genomic data (e.g., whole genome sequencing or sequence capture) have the potential to reveal the tree of life, but it remains challenging to move from sequence data to a clear understanding of evolutionary history, in part due to the computational challenges of phylogenetic estimation using genome-scale data. Supertree methods solve that challenge because they facilitate a divide-and-conquer approach for large-scale phylogeny inference by integrating smaller subtrees in a computationally efficient manner. Here, we combined information from sequence capture and whole-genome phylogenies using supertree methods. However, the available phylogenomic trees had limited overlap so we used taxon-rich (but not phylogenomic) megaphylogenies to weave them together. This allowed us to construct a phylogenomic supertree, with support values, that included 707 bird species (~7% of avian species diversity). We estimated branch lengths using mitochondrial sequence data and we used these branch lengths to estimate divergence times. Our time-calibrated supertree supports radiation of all three major avian clades (Palaeognathae, Galloanseres, and Neoaves) near the Cretaceous-Paleogene (K-Pg) boundary. The approach we used will permit the continued addition of taxa to this supertree as new phylogenomic data are published, and it could be applied to other taxa as well.

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