scholarly journals Evolutionary dynamics of neutral phenotypes under DNA substitution models

2020 ◽  
Author(s):  
Shadi Zabad ◽  
Alan M Moses
Keyword(s):  
Dna Sequences ◽  
Evolutionary Dynamics ◽  
Gc Content ◽  
Stabilizing Selection ◽  
Restoring Force ◽  
Dna Substitution ◽  
Long Term Trends ◽  
The Mean ◽  
Molecular Phenotypes

AbstractWe study the evolution of quantitative molecular traits in the absence of selection. Using a simple theory based on Felsenstein’s 1981 DNA substitution model, we predict a linear restoring force on the mean of an additive phenotype. Remarkably, the mean dynamics are independent of the effect sizes and genotype and are similar to the widely-used OU model for stabilizing selection. We confirm the predictions empirically using additive molecular phenotypes calculated from ancestral reconstructions of putatively unconstrained DNA sequences in primate genomes. We show that the OU model is favoured by inference software even when applied to GC content of unconstrained sequences or simulations of DNA evolution. We predict and confirm empirically that the dynamics of the variance are more complicated than those predicted by the OU model, and show that our results for the restoring force of mutation hold even for non-additive phenotypes, such as number of transcription factor binding sites, longest encoded peptide and folding propensity of the encoded peptide. Our results have implications for efforts to infer selection based on quantitative phenotype dynamics as well as to understand long-term trends in evolution of quantitative molecular traits.

scholarly journals Different long-term trends of the oxygen red 630.0 nm line nightglow intensity as the result of lowering the ionosphere F2 layer

2008 ◽  
Vol 26 (8) ◽  
pp. 2069-2080 ◽  
Author(s):  
N. B. Gudadze ◽  
G. G. Didebulidze ◽  
L. N. Lomidze ◽  
G. Sh. Javakhishvili ◽  
M. A. Marsagishvili ◽  
...  
Keyword(s):  
Electron Density ◽  
Line Intensity ◽  
Peak Height ◽  
Height Distribution ◽  
Theoretical Simulation ◽  
Type Layer ◽  
Long Term Trends ◽  
The Mean ◽  
Long Term Trend

Abstract. Long-term observations of total nightglow intensity of the atomic oxygen red 630.0 nm line at Abastumani (41.75° N, 42.82° E) in 1957–1993 and measurements of the ionosphere F2 layer parameters from the Tbilisi ionosphere station (41.65° N, 44.75° E) in 1963–1986 have been analyzed. It is shown that a decrease in the long-term trend of the mean annual red 630.0 nm line intensity from the pre-midnight value (+0.770±1.045 R/year) to its minimum negative value (−1.080±0.670 R/year) at the midnight/after midnight is a possible result of the observed lowering of the peak height of the ionosphere F2 layer electron density hmF2 (−0.455±0.343 km/year). A theoretical simulation is carried out using a simple Chapman-type layer (damping in time) for the height distribution of the F2 layer electron density. The estimated values of the lowering in the hmF2, the increase in the red line intensity at pre-midnight and its decrease at midnight/after midnight are close to their observational ones, when a negative trend in the total neutral density of the upper atmosphere and an increase in the mean northward wind (or its possible consequence – a decrease in the southward one) are assumed.

scholarly journals An Intelligent Optimization Algorithm for Constructing a DNA Storage Code: NOL-HHO

2020 ◽  
Vol 21 (6) ◽  
pp. 2191 ◽  
Author(s):  
Qiang Yin ◽  
Ben Cao ◽  
Xue Li ◽  
Bin Wang ◽  
Qiang Zhang ◽  
...  
Keyword(s):  
Optimization Algorithm ◽  
Dna Sequences ◽  
Learning Strategy ◽  
Hamming Distance ◽  
Experimental Testing ◽  
Gc Content ◽  
Smooth Transition ◽  
Local Optima ◽  
Dna Storage

The high density, large capacity, and long-term stability of DNA molecules make them an emerging storage medium that is especially suitable for the long-term storage of large datasets. The DNA sequences used in storage need to consider relevant constraints to avoid nonspecific hybridization reactions, such as the No-runlength constraint, GC-content, and the Hamming distance. In this work, a new nonlinear control parameter strategy and a random opposition-based learning strategy were used to improve the Harris hawks optimization algorithm (for the improved algorithm NOL-HHO) in order to prevent it from falling into local optima. Experimental testing was performed on 23 widely used benchmark functions, and the proposed algorithm was used to obtain better coding lower bounds for DNA storage. The results show that our algorithm can better maintain a smooth transition between exploration and exploitation and has stronger global exploration capabilities as compared with other algorithms. At the same time, the improvement of the lower bound directly affects the storage capacity and code rate, which promotes the further development of DNA storage technology.

Assessment of Nonresearch Industry Payments to Otolaryngologists in 2014 and 2015

2018 ◽  
Vol 158 (6) ◽  
pp. 1028-1034 ◽  
Author(s):  
Neil Pathak ◽  
Rance J. T. Fujiwara ◽  
Saral Mehra
Keyword(s):  
Annual Variation ◽  
Public Awareness ◽  
Large Change ◽  
Cross Sectional ◽  
Food And Beverage ◽  
Long Term Trends ◽  
The Mean ◽  
Open Payments ◽  
Made In

Objective To characterize, describe, and compare nonresearch industry payments made to otolaryngologists in 2014 and 2015. Additionally, to describe industry payment variation within otolaryngology and among other surgical specialties. Study Design Retrospective cross-sectional database analysis. Setting Open Payments Database. Subjects and Methods Nonresearch payments made to US otolaryngologists were characterized and compared by payment amount, nature of payment, sponsor, and census region between 2014 and 2015. Payments in otolaryngology were compared with those in other surgical specialties. Results From 2014 to 2015, there was an increase in the number of compensated otolaryngologists (7903 vs 7946) and in the mean payment per compensated otolaryngologist ($1096 vs $1242), as well as a decrease in the median payment per compensated otolaryngologist ($169 vs $165, P = .274). Approximately 90% of total payments made in both years were attributed to food and beverage. Northeast census region otolaryngologists received the highest median payment in 2014 and 2015. Compared with other surgical specialists, otolaryngologists received the lowest mean payment in 2014 and 2015 and the second-lowest and lowest median payment in 2014 and 2015, respectively. Conclusion The increase in the mean payment and number of compensated otolaryngologists can be explained by normal annual variation, stronger industry-otolaryngologist relationships, or improved reporting; additional years of data and improved public awareness of the Sunshine Act will facilitate determining long-term trends. The large change in disparity between the mean and median from 2014 to 2015 suggests greater payment variation. Otolaryngologists continue to demonstrate limited industry ties when compared with other surgical specialists.

Trends in match injury risk in professional male rugby union: a 16-season review of 10 851 match injuries in the English Premiership (2002–2019): the Professional Rugby Injury Surveillance Project

2020 ◽  
pp. bjsports-2020-102529
Author(s):  
Stephen W West ◽  
Lindsay Starling ◽  
Simon Kemp ◽  
Sean Williams ◽  
Matthew Cross ◽  
...  
Keyword(s):  
Injury Risk ◽  
Injury Severity ◽  
Rugby Union ◽  
Injury Surveillance ◽  
Injury Incidence ◽  
Match Play ◽  
Common Activity ◽  
Long Term Trends ◽  
The Mean

ObjectivesThe Professional Rugby Injury Surveillance Project is the largest and longest running rugby union injury surveillance project globally and focuses on the highest level of rugby in England.MethodsWe examined match injuries in professional men’s rugby over the period 2002/2003 to 2018/2019 and described trends in injuries over this time.ResultsOver the period 2002/2003–2018/2019, 10 851 injuries occurred in 1 24 952 hours of match play, equating to a mean of 57 injuries per club per season and one injury per team per match. The mean incidence, severity (days absence) and burden (days absence/1000 hours) of injury were 87/1000 hours (95% CI 82 to 92), 25 days (95% CI 22 to 28) and 2178 days/1000 hours (95% CI 1872 to 2484), respectively. The tackle accounted for 43% injuries with running the second most common activity during injury (12%). The most common injury location was the head/face with an incidence of 11.3/1000 hours, while the location with the highest overall burden was the knee (11.1 days/1000 hours). Long-term trends demonstrated stable injury incidence and proportion of injured players, but an increase in the mean and median severity of injuries. Concussion incidence, severity and burden increased from the 2009/2010 season onwards and from 2011 to 2019 concussion was the most common injury.ConclusionThe rise in overall injury severity and concussion incidence are the most significant findings from this work and demonstrate the need for continued efforts to reduce concussion risk as well as a greater understanding of changes in injury severity over time.

scholarly journals Changes in the reproductive parameters of female harp seals (Pagophilus groenlandicus) in the Northwest Atlantic

2009 ◽  
Vol 67 (2) ◽  
pp. 304-315 ◽  
Author(s):  
Becky Sjare ◽  
Garry B. Stenson
Keyword(s):  
Environmental Factors ◽  
Population Size ◽  
Sexual Maturity ◽  
Reproductive Parameters ◽  
Northwest Atlantic ◽  
Pagophilus Groenlandicus ◽  
Long Term Trends ◽  
The Mean ◽  
The 1950S

Abstract Sjare, B., and Stenson, G. B. 2010. Changes in the reproductive parameters of female harp seals (Pagophilus groenlandicus) in the Northwest Atlantic. – ICES Journal of Marine Science, 67: 304–315. Changes in female harp seal (Pagophilus groenlandicus) reproductive parameters from 1980 to 2004, and long-term trends since the early 1950s, are evaluated. Estimates of the total number of seals in the Northwest Atlantic declined from ∼3.0 million in the 1950s to 1.8 million in the early 1970s, then increased steadily to 5.5 million in 1996, at which relatively stable level it has remained since. Pregnancy rates increased from ∼86% in the 1950s to a high of 98% in the mid-1960s, then declined to ∼65–70% by the early 1990s; the rate then varied between 45 and 70% from 2000 to 2004. Concurrently, the mean age at sexual maturity decreased from 5.8 (s.e = 0.02) years in the mid-1950s to 4.1 (s.e. = 0.02) in the late 1970s, increased to 5.5 (s.e. = 0.03) years by the early 1990s, and peaked at 5.7 (s.e. = 0.01) in 1995. From 2000 to 2004, mean age varied from 4.9 (s.e. = 0.01) to 6.0 (s.e. = 0.01) years. Although the direction of change in each of the parameters was consistent with a density-dependent response, changes in population size explained relatively little of the variability observed, suggesting that other ecological or environmental factors were influential.

scholarly journals The Impact of Improved Thermistor Calibration on the Expendable Bathythermograph Profile Data

2017 ◽  
Vol 34 (9) ◽  
pp. 1947-1961 ◽  
Author(s):  
Marlos Goes ◽  
Elizabeth Babcock ◽  
Francis Bringas ◽  
Peter Ortner ◽  
Gustavo Goni
Keyword(s):  
Small Sample Size ◽  
Heat Content ◽  
Small Sample ◽  
Profile Data ◽  
Expendable Bathythermograph ◽  
Different Types ◽  
Long Term Trends ◽  
The Mean ◽  
The Impact

AbstractExpendable bathythermograph (XBT) data provide one of the longest available records of upper-ocean temperature. However, temperature and depth biases in XBT data adversely affect estimates of long-term trends of ocean heat content and, to a lesser extent, estimates of volume and heat transport in the ocean. Several corrections have been proposed to overcome historical biases in XBT data, which rely on constantly monitoring these biases. This paper provides an analysis of data collected during three recent hydrographic cruises that utilized different types of probes, and examines methods to reduce temperature and depth biases by improving the thermistor calibration and reducing the mass variability of the XBT probes.The results obtained show that the use of individual thermistor calibration in XBT probes is the most effective calibration to decrease the thermal bias, improving the mean thermal bias to less than 0.02°C and its tolerance from 0.1° to 0.03°C. The temperature variance of probes with screened thermistors is significantly reduced by approximately 60% in comparison to standard probes. On the other hand, probes with a tighter weight tolerance did not show statistically significant reductions in the spread of depth biases, possibly because of the small sample size or the sensitivity of the depth accuracy to other causes affecting the analysis.

scholarly journals Shift of subtropical transport barriers explains observed hemispheric asymmetry of decadal trends of age of air

2017 ◽  
Author(s):  
Gabriele P. Stiller ◽  
Federico Fierli ◽  
Felix Ploeger ◽  
Chiara Cagnazzo ◽  
Bernd Funke ◽  
...  
Keyword(s):  
Circulation Pattern ◽  
Transport Time ◽  
Model Calculations ◽  
Model Predictions ◽  
Southward Shift ◽  
Transport Barriers ◽  
Long Term Trends ◽  
The Mean ◽  
Middle Stratosphere

Abstract. In response to global warming the Brewer–Dobson circulation in the stratosphere is expected to accelerate and the mean transport time of air along this circulation to decrease. This would imply a negative stratospheric age of air trend, i.e. an air parcel would need less time to travel from the tropopause to any point in the stratosphere. Age of air as inferred from tracer observations, however, shows zero to positive trends in the Northern midlatitude stratosphere and zonally asymmetric patterns. Using satellite 5 observations and model calculations we show that the observed latitudinal and vertical patterns of the decadal changes of age of air in the lower to middle stratosphere during 2002–2012 are predominantly caused by a southward shift of the circulation pattern of about 5 degrees. After correction for this shift, the observations reveal a hemispherically almost symmetric decrease of age of air in the lower to middle stratosphere up to 800 K of up to −0.25 years over the 2002–2012 period with strongest decrease in the Northern tropics. This net change is consistent with long-term trends from model predictions.

scholarly journals Shift of subtropical transport barriers explains observed hemispheric asymmetry of decadal trends of age of air

2017 ◽  
Vol 17 (18) ◽  
pp. 11177-11192 ◽  
Author(s):  
Gabriele P. Stiller ◽  
Federico Fierli ◽  
Felix Ploeger ◽  
Chiara Cagnazzo ◽  
Bernd Funke ◽  
...  
Keyword(s):  
Circulation Pattern ◽  
Transport Time ◽  
Model Calculations ◽  
Model Predictions ◽  
Southward Shift ◽  
Transport Barriers ◽  
Long Term Trends ◽  
The Mean ◽  
Middle Stratosphere

Abstract. In response to global warming, the Brewer–Dobson circulation in the stratosphere is expected to accelerate and the mean transport time of air along this circulation to decrease. This would imply a negative stratospheric age of air trend, i.e. an air parcel would need less time to travel from the tropopause to any point in the stratosphere. Age of air as inferred from tracer observations, however, shows zero to positive trends in the northern mid-latitude stratosphere and zonally asymmetric patterns. Using satellite observations and model calculations we show that the observed latitudinal and vertical patterns of the decadal changes of age of air in the lower to middle stratosphere during the period 2002–2012 are predominantly caused by a southward shift of the circulation pattern by about 5°. After correction for this shift, the observations reveal a hemispherically almost symmetric decrease of age of air in the lower to middle stratosphere up to 800 K of up to −0.25 years over the 2002–2012 period with strongest decrease in the northern tropics. This net change is consistent with long-term trends from model predictions.

scholarly journals Genomic Signatures in Microbes—Properties and Applications

2011 ◽  
Vol 11 ◽  
pp. 715-725 ◽  
Author(s):  
Jon Bohlin
Keyword(s):  
Dna Sequences ◽  
Gc Content ◽  
Genomic Signature ◽  
Closely Related Species ◽  
Microbial Genomes ◽  
Genomic Signatures ◽  
A Genome ◽  
The Mean ◽  
Microbial Dna ◽  
Genomic Dna Sequence

The ratio of genomic oligonucleotide frequencies relative to the mean genomic AT/GC content has been shown to be similar for closely related species and, therefore, said to reflect a “genomic signature”. The genomic signature has been found to be more similar within genomes than between closely related genomes. Furthermore, genomic signatures of closely related organisms are, in turn, more similar than more distantly related organisms. Since the genomic signature is remarkably stable within a genome, it can be extracted from only a fraction of the genomic DNA sequence. Genomic signatures, therefore, have many applications. The most notable examples include recognition of pathogenicity islands in microbial genomes and identification of hosts from arbitrary DNA sequences, the latter being of great importance in metagenomics. What shapes the genomic signature in microbial DNA has been readily discussed, but difficult to pinpoint exactly. Most attempts so far have mainly focused on correlations fromin silicodata. This mini-review seeks to summarize possible influences shaping the genomic signature and to survey a set of applications.

scholarly journals Global tropopause altitudes in radiosondes and reanalyses

2019 ◽  
Vol 19 (8) ◽  
pp. 5661-5678 ◽  
Author(s):  
Tao Xian ◽  
Cameron R. Homeyer
Keyword(s):  
Climate Change ◽  
Coordinate System ◽  
Lapse Rate ◽  
Vertical Resolution ◽  
Long Term Trends ◽  
The Mean ◽  
The Tropics ◽  
Increasing Trends

Abstract. Accurate depictions of the tropopause and its changes are important for studies on stratosphere–troposphere exchange and climate change. Here, the fidelity of primary lapse-rate tropopause altitudes and double tropopause frequencies in four modern reanalyses (ERA-Interim, JRA-55, MERRA-2, and CFSR) is examined using global radiosonde observations. In addition, long-term trends (1981–2015) in these tropopause properties are diagnosed in both the reanalyses and radiosondes. It is found that reanalyses reproduce observed tropopause altitudes with little bias (typically less than ±150 m) and error comparable to the model vertical resolution. All reanalyses underestimate the double tropopause frequency (up to 30 % lower than observed), with the largest biases found in JRA-55 and the smallest in CFSR. The underestimates in double tropopause frequency are primarily attributable to the coarse vertical resolution of the reanalyses. Significant increasing trends in both tropopause altitude (40–120 m per decade) and double tropopause frequency (≥3 % per decade) were found in both the radiosonde observations and the reanalyses over the 35-year analysis period (1981–2015). ERA-Interim, JRA-55, and MERRA-2 broadly reproduce the patterns and signs of observed significant trends, while CFSR is inconsistent with the remaining datasets. Trends were diagnosed in both the native Eulerian coordinate system of the reanalyses (fixed longitude and latitude) and in a coordinate system where latitude is defined relative to the mean latitude of the tropopause break (the discontinuity in tropopause altitude between the tropics and extratropics) in each hemisphere. The coordinate relative to the tropopause break facilitates the evaluation of tropopause behavior within the tropical and extratropical reservoirs and revealed significant differences in trend estimates compared to the traditional Eulerian analysis. Notably, increasing tropopause altitude trends were found to be of greater magnitude in coordinates relative to the tropopause break, and increasing double tropopause frequency trends were found to occur primarily poleward of the tropopause break in each hemisphere.

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