scholarly journals Further confirmation for unknown archaic ancestry in Andaman and South Asia

2016 ◽  
Author(s):  
Mayukh Mondal ◽  
Ferran Casals ◽  
Partha P. Majumder ◽  
Jaume Bertranpetit
Keyword(s):  
Statistical Treatment ◽  
Data Sets ◽  
Diverse Populations ◽  
African Origin ◽  
Single Wave ◽  
Single Origin ◽  
Sources Of Error ◽  
Out Of Africa ◽  
Improved Model ◽  
Genomic Regions

In a recent paper1, we have derived three main conclusions: i) that all Asian and Pacific populations share a single origin and expansion out of Africa, contradicting an earlier proposal of two independent waves; ii) that populations from South and Southeast Asia harbor a small proportion of ancestry from an unknown extinct hominin – different from the Neanderthal and the Denisovan – which is absent in Europeans; and, iii) that the characteristic distinctive phenotypes (including very short stature) of Andamanese do not reflect an ancient African origin, but have resulted from strong natural selection on genes related to human body size. Although the single wave out of Africa2 and single origin for Asian and Pacific populations have been confirmed3, the existence of admixture with an extinct hominin has been challenged by Skoglund et al.4, as they were unable to replicate our results in their data sets. While we had used a wide variety of statistical methods and data sets from diverse populations to draw our inference, Skoglund et al.4 have used only one method (D-stats5, for the whole genome, not specifically for the relevant genomic regions) and compared only with the Asians, not even with the Europeans. Skoglund et al.4 have alleged that our statistical treatment of the data was faulty and have pointed out some possible sources of error. We have reexamined our data focusing on possible sources of error flagged by Skoglund et al4. We have also performed new analyses. The reexamination and new analyses have bolstered our confidence that our earlier inferences were correct and have resulted in an improved model of introgression of modern humans with a hitherto unknown archaic ancestry. We also propose a possible reason for the inability of Skoglund et al.4 to validate our inference.

scholarly journals An Improved Approach for Reduction of Defect Density Using Optimal Module Sizes

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Dinesh Verma ◽  
Shishir Kumar
Keyword(s):  
Goodness Of Fit ◽  
Defect Density ◽  
Optimal Size ◽  
Data Sets ◽  
Density Parameter ◽  
Proposed Model ◽  
Module Size ◽  
Curve Fitting Method ◽  
Improved Model ◽  
Effective Distribution

Nowadays, software developers are facing challenges in minimizing the number of defects during the software development. Using defect density parameter, developers can identify the possibilities of improvements in the product. Since the total number of defects depends on module size, so there is need to calculate the optimal size of the module to minimize the defect density. In this paper, an improved model has been formulated that indicates the relationship between defect density and variable size of modules. This relationship could be used for optimization of overall defect density using an effective distribution of modules sizes. Three available data sets related to concern aspect have been examined with the proposed model by taking the distinct values of variables and parameter by putting some constraint on parameters. Curve fitting method has been used to obtain the size of module with minimum defect density. Goodness of fit measures has been performed to validate the proposed model for data sets. The defect density can be optimized by effective distribution of size of modules. The larger modules can be broken into smaller modules and smaller modules can be merged to minimize the overall defect density.

EFFECTS OF THE ELECTRONIC BAND SHAPE OF PALLADIUM METAL ON THE PROTON MODEL FOR HYDROGEN ABSORPTION

1965 ◽  
Vol 43 (6) ◽  
pp. 1665-1671 ◽  
Author(s):  
J. W. Simons ◽  
Ted B. Flanagan
Keyword(s):  
Hydrogen Absorption ◽  
Statistical Treatment ◽  
Original Model ◽  
Band Shape ◽  
Electronic Band ◽  
Critical Isotherm ◽  
Critical Composition ◽  
Improved Model ◽  
Electron Donation ◽  
Palladium Metal

The statistical treatment of the proton model for hydrogen absorption by palladium is extended to include a variation of the electron donation energy with hydrogen content, as determined by a density of states function for the combined 4d- and 5s-bands for palladium. This improved model gives better agreement with the high pressure limiting solubility data and the observed critical composition than the original model, when both are fitted to the critical isotherm by the same method. An apparent anomaly in the variation of the isosteric enthalpy of absorption with content is explained by the improved model.

scholarly journals Model – TCCON comparisons of column-averaged methane with a focus on the stratosphere

2016 ◽  
Author(s):  
Andreas Ostler ◽  
Ralf Sussmann ◽  
Prabir K. Patra ◽  
Sander Houweling ◽  
Marko De Bruine ◽  
...  
Keyword(s):  
Atmospheric Chemistry ◽  
Transport Model ◽  
Meteorological Data ◽  
Michelson Interferometer ◽  
Total Carbon ◽  
Data Sets ◽  
Transport Models ◽  
Improved Model ◽  
The Impact ◽  
Chemistry Experiment

Abstract. The distribution of methane (CH4) in the stratosphere can be a major driver of spatial variability in the dry-air column-averaged CH4 mixing ratio (XCH4), which is being measured increasingly for the assessment of CH4 surface emissions. Chemistry-transport models (CTMs) therefore need to simulate the tropospheric and stratospheric fractional columns of XCH4 accurately for estimating surface emissions from XCH4. Simulations from three CTMs are tested against XCH4 observations from the Total Carbon Column Network (TCCON). We analyze how the model-TCCON agreement in XCH4 depends on the model representation of stratospheric CH4 distributions. Model equivalents of TCCON XCH4 are computed with stratospheric CH4 fields from both the model simulations and from satellite-based CH4 distributions from MIPAS (Michelson Interferometer for Passive Atmospheric Sounding) and MIPAS CH4 fields adjusted to ACE-FTS (Atmospheric Chemistry Experiment Fourier Transform Spectrometer) observations. In comparison to simulated model fields we find an improved model-TCCON XCH4 agreement for all models with MIPAS-based stratospheric CH4 fields. For the Atmospheric Chemistry Transport Model (ACTM) the average XCH4 bias is significantly reduced from 38.1 ppb to 13.7 ppb, whereas small improvements are found for the models TM5 (Transport Model, version 5; from 8.7 ppb to 4.3 ppb), and LMDz (Laboratoire de Météorologie Dynamique model with Zooming capability; from 6.8 ppb to 4.3 ppb), respectively. MIPAS stratospheric CH4 fields adjusted to ACE-FTS reduce the average XCH4 bias for ACTM (3.3 ppb), but increase the average XCH4 bias for TM5 (10.8 ppb) and LMDz (20.0 ppb). These findings imply that the range of satellite-based stratospheric CH4 is insufficient to resolve a possible stratospheric contribution to differences in total column CH4 between TCCON and TM5 or LMDz. Applying transport diagnostics to the models indicates that model-to-model differences in the simulation of stratospheric transport, notably the age of stratospheric air, can largely explain the inter-model spread in stratospheric CH4 and, hence, its contribution to XCH4. This implies that there is a need to better understand the impact of individual model transport components (e.g., physical parameterization, meteorological data sets, model horizontal/vertical resolution) on modeled stratospheric CH4.

Accuracy of School Screenings in the Identification of Minimal Sensorineural Hearing Loss

2014 ◽  
Vol 23 (4) ◽  
pp. 365-373 ◽  
Author(s):  
Jeanne Dodd-Murphy ◽  
Walter Murphy ◽  
Fred H. Bess
Keyword(s):  
Hearing Loss ◽  
Prospective Study ◽  
Sensorineural Hearing Loss ◽  
Sensorineural Hearing ◽  
School Age Children ◽  
Data Sets ◽  
School Age ◽  
Diverse Populations ◽  
Referral Rates ◽  
Referral Criterion

Purpose The goal of this study was to investigate how the use of a 25 dB HL referral criterion in school screenings affects the identification of hearing loss categorized as minimal sensorineural hearing loss (MSHL). Method A retrospective study applied screening levels of 20 and 25 dB HL at 1000, 2000, and 4000 Hz in each ear to previously obtained pure-tone thresholds for 1,475 school-age children. In a separate prospective study, 1,704 children were screened at school under typical conditions, and a subsample had complete audiological evaluations. Referral rates, sensitivity, and specificity were calculated for each screening level. Results Referral rates varied by grade and criterion level, with comparable results between the two data sets. In both studies, when the screening level increased, the sensitivity to MSHL declined markedly, whereas specificity increased in the prospective study. Conclusions Screening at 25 dB yields poor sensitivity to MSHL. Converging evidence from these diverse populations supports using the 20 dB level to help identify MSHL. Multistage screening is recommended to limit referral rates. Even at 20 dB HL, cases of MSHL may be missed. Audiologists should encourage parents, educators, and speech–language pathologists to refer children suspected of hearing difficulty for complete audiological evaluations even if they pass school screenings.

Predicting Flowering of Rhizome Johnsongrass (Sorghum halepense) Populations Using a Temperature-dependent Model

Weed Science ◽  
1996 ◽  
Vol 44 (2) ◽  
pp. 266-272 ◽  
Author(s):  
David L. Holshouser ◽  
James M. Chandler
Keyword(s):  
Rate Equation ◽  
Model Performance ◽  
Population Level ◽  
Weibull Function ◽  
Data Sets ◽  
Temperature Dependent ◽  
Independent Field ◽  
Dependent Model ◽  
Improved Model ◽  
Temperature Dependent Model

Research was conducted to formulate a temperature-dependent population-level model for rhizome johnsongrass flowering. A nonlinear poikilotherm rate equation was used to describe development as a function of temperature and a temperature-independent Weibull function was used to distribute development times for the population. Johnsongrass flowering data were collected under constant temperature conditions to parameterize the poikilotherm rate equation and Weibull function. Coupling the poikilotherm rate equation with the Weibull function resulted in a population level temperature-dependent model. The model was validated against independent field data sets. The model accurately predicted rhizome johnsongrass flowering from plants emerging in the spring. The model performed poorly for plants emerging in summer. Adjustments to the high-temperature inhibition parameter of the poikilotherm rate equation improved model performance in the summer without affecting spring predictions.

scholarly journals Carriers of mitochondrial DNA macrohaplogroup L3 basic lineages migrated back to Africa from Asia around 70,000 years ago

2017 ◽  
Author(s):  
Vicente M. Cabrera ◽  
Patricia Marrero ◽  
Khaled K. Abu-Amero ◽  
Jose M. Larruga
Keyword(s):  
Y Chromosome ◽  
Fossil Record ◽  
Climatic Conditions ◽  
African Origin ◽  
Modern Humans ◽  
Frequency Distributions ◽  
Human Movements ◽  
Anatomically Modern Humans ◽  
Out Of Africa ◽  
Southern Route

ABSTRACTBackgroundAfter three decades of mtDNA studies on human evolution the only incontrovertible main result is the African origin of all extant modern humans. In addition, a southern coastal route has been relentlessly imposed to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, that out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion. Consistent with the fossil record, we have dated it around 125 kya. To help bridge differences between the molecular and fossil record ages, in this article we assess the possibility that mtDNA macrohaplogroup L3 matured in Eurasia and returned to Africa as basic L3 lineages around 70 kya.ResultsThe coalescence ages of all Eurasian (M,N) and African L3 lineages, both around 71 kya, are not significantly different. The oldest M and N Eurasian clades are found in southeastern Asia instead near of Africa as expected by the southern route hypothesis. The split of the Y-chromosome composite DE haplogroup is very similar to the age of mtDNA L3. A Eurasian origin and back migration to Africa has been proposed for the African Y-chromosome haplogroup E. Inside Africa, frequency distributions of maternal L3 and paternal E lineages are positively correlated. This correlation is not fully explained by geographic or ethnic affinities. It seems better to be the result of a joint and global replacement of the old autochthonous male and female African lineages by the new Eurasian incomers.ConclusionsThese results are congruent with a model proposing an out-of-Africa of early anatomically modern humans around 125 kya. A return to Africa of Eurasian fully modern humans around 70 kya, and a second Eurasian global expansion by 60 kya. Climatic conditions and the presence of Neanderthals played key roles in these human movements.

scholarly journals Genetic Associations in Four Decades of Multi-Environment Trials Reveal Agronomic Trait Evolution in Common Bean

2019 ◽  
Author(s):  
Alice H. MacQueen ◽  
Jeffrey W. White ◽  
Rian Lee ◽  
Juan M. Osorno ◽  
Jeremy Schmutz ◽  
...  
Keyword(s):  
Common Bean ◽  
Crop Improvement ◽  
Genetic Research ◽  
The United States ◽  
Genetic Effects ◽  
Data Sets ◽  
Genetic Associations ◽  
Phenotypic Data ◽  
Multiple Phenotypes ◽  
Genomic Regions

AbstractMulti-environment trials (METs) are widely used to assess the performance of promising crop germplasm. Though seldom designed to elucidate genetic mechanisms, MET datasets are often much larger than could be duplicated for genetic research and, given proper interpretation, may offer valuable insights into the genetics of adaptation across time and space. The Cooperative Dry Bean Nursery (CDBN) is a MET for common bean (Phaseolus vulgaris) grown for over 70 years in the United States and Canada, consisting of 20 to 50 entries each year at 10 to 20 locations. The CBDN provides a rich source of phenotypic data across entries, years, and locations that is amenable to genetic analysis. To study stable genetic effects segregating in this MET, we conducted genome-wide association (GWAS) using best linear unbiased predictions (BLUPs) derived across years and locations for 21 CDBN phenotypes and genotypic data (1.2M SNPs) for 327 CDBN genotypes. The value of this approach was confirmed by the discovery of three candidate genes and genomic regions previously identified in balanced GWAS. Multivariate adaptive shrinkage (mash) analysis, which increased our power to detect significant correlated effects, found significant effects for all phenotypes. The first use of mash on an agricultural dataset discovered two genomic regions with pleiotropic effects on multiple phenotypes, likely selected on in pursuit of a crop ideotype. Overall, our results demonstrate that by applying multiple statistical genomic approaches on data mined from MET phenotypic data sets, significant genetic effects that define genomic regions associated with crop improvement can be discovered.

scholarly journals CHIPIN: ChIP-seq inter-sample normalization based on signal invariance across transcriptionally constant genes

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Lélia Polit ◽  
Gwenneg Kerdivel ◽  
Sebastian Gregoricchio ◽  
Michela Esposito ◽  
Christel Guillouf ◽  
...  
Keyword(s):  
Signal To Noise Ratio ◽  
R Package ◽  
Superior Performance ◽  
Open Chromatin ◽  
Data Sets ◽  
Drug Treatments ◽  
On Chip ◽  
Genomic Regions ◽  
Signal Normalization ◽  
User Friendly

Abstract Background Multiple studies rely on ChIP-seq experiments to assess the effect of gene modulation and drug treatments on protein binding and chromatin structure. However, most methods commonly used for the normalization of ChIP-seq binding intensity signals across conditions, e.g., the normalization to the same number of reads, either assume a constant signal-to-noise ratio across conditions or base the estimates of correction factors on genomic regions with intrinsically different signals between conditions. Inaccurate normalization of ChIP-seq signal may, in turn, lead to erroneous biological conclusions. Results We developed a new R package, CHIPIN, that allows normalizing ChIP-seq signals across different conditions/samples when spike-in information is not available, but gene expression data are at hand. Our normalization technique is based on the assumption that, on average, no differences in ChIP-seq signals should be observed in the regulatory regions of genes whose expression levels are constant across samples/conditions. In addition to normalizing ChIP-seq signals, CHIPIN provides as output a number of graphs and calculates statistics allowing the user to assess the efficiency of the normalization and qualify the specificity of the antibody used. In addition to ChIP-seq, CHIPIN can be used without restriction on open chromatin ATAC-seq or DNase hypersensitivity data. We validated the CHIPIN method on several ChIP-seq data sets and documented its superior performance in comparison to several commonly used normalization techniques. Conclusions The CHIPIN method provides a new way for ChIP-seq signal normalization across conditions when spike-in experiments are not available. The method is implemented in a user-friendly R package available on GitHub: https://github.com/BoevaLab/CHIPIN

scholarly journals Multiple isotopic models using various kinetic fractionation coefficients to estimateδ18O of leaf water

2018 ◽  
Author(s):  
Yonge Zhang ◽  
Xinxiao Yu ◽  
Lihua Chen ◽  
Guodong Jia
Keyword(s):  
Steady State ◽  
Time Scale ◽  
Model Performance ◽  
Special Care ◽  
Leaf Water ◽  
Data Sets ◽  
Kinetic Fractionation ◽  
Improved Model ◽  
Material Exchange ◽  
Good Agreement

AbstractInvestigation ofδ18O of leaf water may improve our understanding of the evapotranspiration partitioning and material exchange between the inside and outside of leaves. In this study,δ18O of bulk leaf water (δL,b) was estimated by both isotopic–steady–state (ISS) and non–steady–state (NSS) assumptions considering the Péclet effect. Specifically, we carefully modified kinetic fractionation coefficients (αk). The results showed that the Péclet effect is required to predictδL,b. On the diel time scale, both NSS assumption + Péclet effect (NSS + P) and ISS assumption + Péclet effect (ISS + P) using modifiedαk(αk–modified) forδL,bshowed a good agreement with observedδL,b(p> 0.05). When using previously proposedαk, however, both NSS + P and ISS + P were not reliable estimators ofδL,b(p< 0.05). On a longer time scale (days), estimates of daily meanδL,bfrom ISS + P outperformed the estimates from NSS + P when using the sameαkvalues. Also, the employment ofαk–modifiedimproved model performance in predicting daily meanδL,bcompared to the use of previously proposedαk. Clearly, special care must be taken concerningαkwhen using isotopic models to estimateδL,b.HighlightFor hourly and daily mean data sets, the employment of modified kinetic fractionation coefficients significantly improved model performance forδ18O of bulk leaf water.

Sign in / Sign up

Export Citation Format

Share Document