Bias Variation Research Articles

Enhanced effective codon numbers to understand codon usage bias

Codon usage bias is a well recognized phenomenon but the relative influence of its major causes: G+C content, mutational biases, and selection, are often difficult to disentangle. This paper presents methods to calculate modified effective codon numbers that allow the investigation of the sources of codon bias and how genes or organisms have their codon biases shaped. In particular, it demonstrates that variation in codon usage bias across organisms is likely driven more by likely mutational forces while the variation in codon usage bias within genomes is likely driven by codon selectional forces.

Aggression induced by ornament similarity is limited to females in a mutually ornamented fish, Betta brownorum

Ornamentation found in both sexes, or mutual ornamentation, can be used as a threat signal towards rivals or to bias aggression towards those sharing preferences for mates or other resources. The widespread male bias in ornamentation suggests that sexual selection for these competitive functions is stronger in males, but these functions are rarely compared between the sexes. We investigated intrasexual contests in a mutually ornamented fish, Betta brownorum , that uniquely has both male bias and high intrasexual variation in the presence and size of side blotches. Neither blotch size nor body size predicted the winner in either sex. The frequency of lateral display increased with opponent body size in females. Physical attacks increased when facing similarly blotched opponents only in females. These results suggest that nonsexual social selection contributes more to the maintenance of blotches than sexual selection, as the latter predicts the threat signal and/or aggression bias mainly in the sex with greater ornamentation. Our study highlights that smaller female ornaments can have social functions that are distinct from those of male ornaments and may be partially maintained by social selection in many other systems. • A mutually ornamented fish, Betta brownorum , shows high ornament variation. • We found no advantage of large blotches in winning contests. • Similar blotch sizes between contestants increased physical attacks only in females. • Nonsexual social selection is suggested to be influential in female B. brownorum .

Intragenomic variation in non-adaptive nucleotide biases causes underestimation of selection on synonymous codon usage.

Patterns of non-uniform usage of synonymous codons vary across genes in an organism and between species across all domains of life. This codon usage bias (CUB) is due to a combination of non-adaptive (e.g. mutation biases) and adaptive (e.g. natural selection for translation efficiency/accuracy) evolutionary forces. Most models quantify the effects of mutation bias and selection on CUB assuming uniform mutational and other non-adaptive forces across the genome. However, non-adaptive nucleotide biases can vary within a genome due to processes such as biased gene conversion (BGC), potentially obfuscating signals of selection on codon usage. Moreover, genome-wide estimates of non-adaptive nucleotide biases are lacking for non-model organisms. We combine an unsupervised learning method with a population genetics model of synonymous coding sequence evolution to assess the impact of intragenomic variation in non-adaptive nucleotide bias on quantification of natural selection on synonymous codon usage across 49 Saccharomycotina yeasts. We find that in the absence of a priori information, unsupervised learning can be used to identify genes evolving under different non-adaptive nucleotide biases. We find that the impact of intragenomic variation in non-adaptive nucleotide bias varies widely, even among closely-related species. We show that the overall strength and direction of translational selection can be underestimated by failing to account for intragenomic variation in non-adaptive nucleotide biases. Interestingly, genes falling into clusters identified by machine learning are also physically clustered across chromosomes. Our results indicate the need for more nuanced models of sequence evolution that systematically incorporate the effects of variable non-adaptive nucleotide biases on codon frequencies.

Seasonal extrema of sea surface temperature in CMIP6 models

Abstract. CMIP6 model sea surface temperature (SST) seasonal extrema averaged over 1981–2010 are assessed against the World Ocean Atlas (WOA18) observational climatology. We propose a mask to identify and exclude regions of large differences between three commonly used climatologies (WOA18, WOCE-Argo Global Hydrographic climatology (WAGHC) and the Hadley Centre Sea Ice and Sea Surface Temperature data set (HadISST)). The biases in SST seasonal extrema are largely consistent with the annual mean SST biases. However, the amplitude and spatial pattern of SST bias vary seasonally in the 20 CMIP6 models assessed. Large seasonal variations in the SST bias occur in eastern boundary upwelling regions, polar regions, the North Pacific and the eastern equatorial Atlantic. These results demonstrate the importance of evaluating model performance not simply against annual mean properties. Models with greater vertical resolution in their ocean component typically demonstrate better representation of SST extrema, particularly seasonal maximum SST. No significant relationship of SST seasonal extrema with horizontal ocean model resolution is found.

Development and validation of an isoform-independent monoclonal antibody–based ELISA for measurement of lipoprotein(a)

The study aims were to develop a new isoform-independent enzyme-linked immunoassay (ELISA) for the measurement of lipoprotein(a) [Lp(a)], validate its performance characteristics, and demonstrate its accuracy by comparison with the gold-standard ELISA method and an LC-MS/MS candidate reference method, both developed at the University of Washington. The principle of the new assay is the capture of Lp(a) with monoclonal antibody LPA4 primarily directed to an epitope in apolipoprotein(a) KIV2 and its detection with monoclonal antibody LPA-KIV9 directed to a single antigenic site present on KIV9. Validation studies were performed following the guidelines of the Clinical Laboratory Improvement Amendments and the College of American Pathologists. The analytical measuring range of the LPA4/LPA-KIV9 ELISA is 0.27–1,402 nmol/L, and the method meets stringent criteria for precision, linearity, spike and recovery, dilutability, comparison of plasma versus serum, and accuracy. Method comparison with both the gold-standard ELISA and the LC-MS/MS method performed in 64 samples with known apolipoprotein(a) isoforms resulted in excellent correlation with both methods (r=0.987 and r=0.976, respectively). Additionally, the variation in apolipoprotein(a) size accounted for only 0.2% and 2.2% of the bias variation, respectively, indicating that the LPA4/LPA-KIV9 ELISA is not affected by apolipoprotein(a) size polymorphism. Peptide mapping and competition experiments demonstrated that the measuring monoclonal antibodies used in the gold-standard ELISA (a-40) and in the newly developed ELISA (LPA-KIV9) are directed to the same epitope, 4076LETPTVV4082, on KIV9. In conclusion, no statistically or clinically significant bias was observed between Lp(a) measurements obtained by the LPA4/LPA-KIV9 ELISA and those obtained by the gold-standard ELISA or LC-MS/MS, and therefore, the methods are considered equivalent.

Horizon Bias and the Term Structure of Equity Returns

AbstractWe label the degree to which individuals are more optimistic at long horizons relative to short horizons as the horizon bias. We examine whether time-series variation in the horizon bias can explain the time-series variation in the equity term structure. We use analyst earnings forecasts to measure the degree of the horizon bias in the stock market. Consistent with the intuition from a stylized present value model, we find that periods of above-average horizon bias are associated with negative term premiums, whereas periods of below-average horizon bias are associated with positive term premiums.Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.

OPTIMIZATION OF COLD SPLICING PARAMETERS IN CONVEYOR BELT JOINTS ON SHEAR STRENGTH USING TAGUCHI METHOD

In the manufacturing industries, the main problem of material handling process using conveyor belt. Belt that continuously work will have damage or failure, so it repair by cold splicing. The purpose of this study is to see the effect of cold splicing parameters on the shear strength of conveyor belt joints based on variations in the number of belts, bias cut and adhesive thickness. Variations in the number of ply belts used are 2 ply, 3 ply and 4 ply, variations of cut bias 0.3xB, 0.6xB and 0.9xB and variations in the thickness of the adhesive which are 1 mm, 2 mm and 3 mm. This research was conducted experimentally using the Taguchi method based on shear test data using the Universal Testing Machine. Based on ANOVA value, the number of belt ply was high contribution by 86.22% with F-value = 155.3 and bias cut was lowest contribution by 0.23%.

Toward traceable XCT measurement of AM lattice structures: Uncertainty in calibrated reference object measurement

Lattice structures created via additive manufacturing are of interest in several demanding industries, however the qualification of these components via X-ray computed tomography (XCT) is limited due to traceability requirements. In this work, a novel measurement reference object is presented to study task specific uncertainty in the XCT measurement of a simplified lattice structure. The design of this reference object, the calibration routines, and XCT acquisition are described. The description of uncertainty calculation is presented. The methodology for data sampling, registration, and measurement is detailed. The measurement results are tested for normality and show variations in the underlying distribution for different measurands. A discussion on uncertainty variation and normality of measurements is then presented. Variations in measurement bias and uncertainty are analyzed across various features of the reference object. It is shown that the measurement uncertainty and bias are not consistent across pin diameter measurement, indicating the need for similarity between the reference object and subsequent component measurements.

Thermal hysteresis of magnetization in NiFe/IrMn exchange-biased ferromagnet

Magnetization reversal in NiFe/IrMn exchange-biased thin films was investigated under thermal cycling in an external magnetic field, applied opposite to the direction of the exchange bias field. Thermal hysteresis of magnetization accompanied by changes in magnetization polarity was observed in the applied field close to the exchange bias value. This effect appears when thermally induced variations of the exchange bias exceed the corresponding variations in coercivity. The amplitude of magnetization reversal in NiFe/IrMn structures exceeds ∼100 times the corresponding amplitude in spin-crossover molecular compounds. The observed bistability of the magnetic state, revealed by thermal hysteresis, gradually disappears with an increase in the number of cooling–heating thermal cycles, that indicates an irreversible quenching of the interfacial magnetization configuration. This effect paves the way for the creation of a new class of switching devices with thermally assisted bistability in the ferromagnetic state.

Anti-Asian Xenophobia, Hate Crime Victimization, and Fear of Victimization During the COVID-19 Pandemic.

While the World Health Organization advised against referring to COVID-19 using racial overtones, as the COVID-19 pandemic spread, many disparagingly called it the “Wuhan virus,” the “Chinese virus,” and other terms. In this context, the FBI warned police agencies about an expected increase in anti-Asian hate crimes during the early months of the pandemic. But, while some researchers and media outlets discussed these potential increases at length, very few studies have been able to directly assess the nature of anti-Asian hate and bias victimization during the pandemic. Following this, the current study directly examines variation in anti-Asian bias and victimization in the United States during the COVID-19 pandemic. Specifically, this research presents results from two studies using a survey of 3,163 non-Asian and 575 Asian American and Pacific Islander respondents, respectively. The first study examines the prevalence of anti-Asian xenophobia among the non-Asian sample and assesses differences in these prejudicial attitudes across respondent characteristics, while the second study examines variation in experiences with bias during the pandemic among the Asian sample. The results illustrate the ubiquity of anti-Asian sentiment, suggesting that those who indicate greater fear of the pandemic report more prejudicial attitudes, as well as important racial differences in these patterns. The results also demonstrate the extent to which the pandemic has impacted individual experiences with anti-Asian bias victimization, such that more than one-third of Asian respondents report bias victimization during the pandemic, and more than half of Asian respondents report that they know someone who has been victimized. These patterns have important implications for addressing COVID-19-related hate crime moving forward.

Validation of the PPVT–5 for Chinese-English bilingual learners: Application of cross-classified mixed effects model

Despite the wide use of the Peabody Picture Vocabulary Test (PPVT) in second language acquisition and bilingual studies, very few validation studies have been conducted in bilingual contexts, especially for Chinese-English bilinguals. This study was designed to evaluate the validity evidence of the newest version of the series, the PPTV-5, for Chinese-English bilingual first graders in British Columbia, Canada. Validation in this study was an exercise of identifying and explaining sources of expected and unexpected score variations. Cross-classified mixed effects models (CCMEM) were employed to evaluate multiple sources of validity evidence in terms of demographic aspects (i.e., gender, school type, home language, and immigration background), lexical features, and test design. Results showed that there was no bias or unexpected score variations due to gender, school type, and home language. Expected score variations attributed to immigration background, lexical features and test design supported the use of PPVT-5 among Chinese-Bilingual children. In conclusion, PPVT-5 is a valid tool for assessing Chinese-English bilingual children's English receptive vocabulary in Canada.

THE IMPACTS OF TASK COMPLEXITY, OVERCONFIDENCE, CONFIRMATION BIAS, CUSTOMER INFLUENCE, AND ANCHORING ON VARIATIONS IN REAL ESTATE VALUATIONS

Real estate valuation relies on real estate appraisers’ accurate assessments, which reflects the need to improve the objectivity of the valuation process. From the perspective of behavioral economics, appraisers are prone to numerous behavioral conflicts that could result in variations in their valuations. This study investigates the impacts of task complexity, overconfidence, confirmation bias, client influence, and anchoring on variations in real estate valuations. An online questionnaire was administered to 272 members of the Taiwan Real Estate Appraisers Association LINE group. Structural equation modeling was employed for analysis. A total of 150 valid responses were collected, yielding a valid response rate of 55.15%. The empirical results revealed that cognitive bias and client influence have significant and positive impacts on anchoring. Task complexity, overconfidence, and customer influence have significant and positive impacts on valuation variation. In addition to being the first study to explore the relationship between task complexity and valuation variation, this study also explored unconventional issues, such as the relationships between overconfidence, confirmation bias, and valuation variation. The results highlight the salience and value of behavioral economics-based analyses in empirical research on real estate valuation.

Evaluation of the causes of sex disparity in heart failure trials

ObjectivesCardiovascular disease is one of the leading causes of mortality and morbidity in women. Despite this, even in contemporary research, female patients are poorly represented in trials. This study aimed...

Personalized local SAR prediction for parallel transmit neuroimaging at 7T from a single T1-weighted dataset.

PurposeParallel RF transmission (PTx) is one of the key technologies enabling high quality imaging at ultra‐high fields (≥7T). Compliance with regulatory limits on the local specific absorption rate (SAR) typically involves over‐conservative safety margins to account for intersubject variability, which negatively affect the utilization of ultra‐high field MR. In this work, we present a method to generate a subject‐specific body model from a single T1‐weighted dataset for personalized local SAR prediction in PTx neuroimaging at 7T.MethodsMulti‐contrast data were acquired at 7T (N = 10) to establish ground truth segmentations in eight tissue types. A 2.5D convolutional neural network was trained using the T1‐weighted data as input in a leave‐one‐out cross‐validation study. The segmentation accuracy was evaluated through local SAR simulations in a quadrature birdcage as well as a PTx coil model.ResultsThe network‐generated segmentations reached Dice coefficients of 86.7% ± 6.7% (mean ± SD) and showed to successfully address the severe intensity bias and contrast variations typical to 7T. Errors in peak local SAR obtained were below 3.0% in the quadrature birdcage. Results obtained in the PTx configuration indicated that a safety margin of 6.3% ensures conservative local SAR estimates in 95% of the random RF shims, compared to an average overestimation of 34% in the generic “one‐size‐fits‐all” approach.ConclusionA subject‐specific body model can be automatically generated from a single T1‐weighted dataset by means of deep learning, providing the necessary inputs for accurate and personalized local SAR predictions in PTx neuroimaging at 7T.

Improved attitude estimation accuracy by data fusion of a MEMS MARG sensor and a low-cost GNSS receiver

To obtain precise and continuous attitude information, this paper proposed a data fusion scheme that exploits the complementary advantages of a microelectromechanical system (MEMS) magnetic, angular rate, and gravity (MARG) sensor and a low-cost global navigation satellite system (GNSS) receiver. A quaternion-based error state Kalman filter is designed to integrate the different data sources, where the attitude error and gyro bias variation are taken as the error states. The gyro-measured angular rates are continuously integrated to propagate the attitude quaternion, while the accelerometer and magnetometer readings or the GNSS pitch and heading angles estimated by the precise carrier phase observations are utilized to perform the measurement update. The system kinematic model remains constant when the aiding source changes, only the measurement model alternates accordingly. A vehicular dynamical test was conducted to evaluate the proposed algorithm, the test results show that the attitude estimation accuracy of the integrated algorithm is apparently improved.

Empirical Map-Based Nonergodic Models of Site Response in the Greater Los Angeles Area

ABSTRACTWe develop empirical estimates of site response at seismic stations in the Los Angeles area using recorded ground motions from 414 M 3–7.3 earthquakes in southern California. The data are from a combination of the Next Generation Attenuation-West2 project, the 2019 Ridgecrest earthquakes, and about 10,000 newly processed records. We estimate site response using an iterative mixed-effects residuals partitioning approach, accounting for azimuthal variations in anelastic attenuation and potential bias due to spatial clusters of colocated earthquakes. This process yields site response for peak ground acceleration, peak ground velocity, and pseudospectral acceleration relative to a 760 m/s shear-wave velocity (VS) reference condition. We employ regression kriging to generate a spatially continuous site response model, using the linear site and basin terms from Boore et al. (2014) as the background model, which depend on VS30 and depth to the 1 km/s VS isosurface. This is different from past approaches to nonergodic models, in which spatially varying coefficients are regressed. We validate the model using stations in the Community Seismic Network (CSN) that are in the middle of our model spatial domain but were not considered in model development, finding strong agreement between the interpolated model and CSN data for long periods. Our model could be implemented in regional seismic hazard analyses, which would lead to improvements especially at long return periods. Our site response model also has potential to improve both ground-motion accuracy and warning times for the U.S. Geological Survey ShakeAlert earthquake early warning (EEW) system. For a point-source EEW simulation of the 1994 M 6.7 Northridge earthquake, our model produces ground motions more consistent with the ground-truth ShakeMap and would alert areas with high population density such as downtown Los Angeles at lower estimated magnitudes (i.e., sooner) than an ergodic model for a modified Mercalli intensity 4.5 alerting threshold.

Kingdom-Wide Analysis of FungalProtein-Coding and tRNA Genes Reveals Conserved Patterns of Adaptive Evolution.

Protein-coding genes evolved codon usage bias due to the combined but uneven effects of adaptive and nonadaptive influences. Studies in model fungi agree on codon usage bias as an adaptation for fine-tuning gene expression levels; however, such knowledge is lacking for most other fungi. Our comparative genomics analysis of over 450 species supports codon usage and transfer RNAs (tRNAs) as coadapted for translation speed and this is most likely a realization of convergent evolution. Rather than drift, phylogenetic reconstruction inferred adaptive radiation as the best explanation for the variation of interspecific codon usage bias. Although the phylogenetic signals for individual codon and tRNAs frequencies are lower than expected by genetic drift, we found remarkable conservation of highly expressed genes being codon optimized for translation by the most abundant tRNAs, especially by inosine-modified tRNAs. As an application, we present a sequence-to-expression neural network that uses codons to reliably predict highly expressed transcripts. The kingdom Fungi, with over a million species, includes many key players in various ecosystems and good targets for biotechnology. Collectively, our results have implications for better understanding the evolutionary success of fungi, as well as informing the biosynthetic manipulation of fungal genes.

Relative magnitude of two Northern Hawk-Owl (Surnia ulula) irruptions to southern Norway: comparison of citizen data and survey data

Cover photo: Northern Hawk-Owl Surnia ulula. Photo: Terje Lislevand. 
 The Northern Hawk-Owl Surnia ulula occurs as an irruptive species to southern parts of Fennoscandia. Large numbers of individuals were recorded in the autumns of 2016 and 2020 but assessing the relative magnitude of irruptions is challenging. Systematic surveys allow direct comparisons but are time-consuming and will therefore be limited in time and space. Citizen data may provide large amounts of information for wide areas but may in particular suffer from spatial biases in the observation effort of birdwatchers. I compared the 2016 and 2020 irruptions of Northern Hawk-Owls to southern Norway, and found that citizen data indicated that numbers in 2016 were ca. 2–3 times larger than in 2020. However, the relative magnitude differed geographically, and the 2016 irruption was larger in western and southern counties, whereas the difference was smaller in eastern counties (in particular in Innlandet county). Systematic surveys in eastern regions (Oslo and Akershus) indicated that Northern Hawk-Owl densities were similar in the two irruption years. Overall, Northern Hawk-Owls were recorded at the same rate (approximately one owl per 16 km), and density was estimated to be 0.09–0.18 individuals/km2 in 2016 and 0.08–0.13 individuals/km2 in 2020. Thus, citizen data and survey data from the same geographical region concurred. However, due to the geographical variation in relative irruption size and spatial variation in observer density and biases in observation effort, the overall difference between the two years is difficult to assess. The 2016 irruption was likely larger than the 2020 irruption, but the difference was probably smaller than suggested by citizen data.

Total Column Water Vapor From INSAT-3D: Assessments With Ground-Based GNSS Receivers and GMI Datasets at Different Temporal Scales

The quality of the total column water vapor (TCWV) data retrieved from the Indian national satellite (INSAT) system series (INSAT-3D) and its variation at different temporal scales have been evaluated. The reference TCWV dataset is obtained from four ground-based global navigation satellite system (GNSS) receivers and over the entire Indian subcontinent from a global precipitation measurement (GPM) microwave imager (GMI) that uses global analysis (GANAL) model data. TCWV comparison of INSAT-3D, GPM-GMI with GNSS show higher correlations for GPM-GMI than INSAT-3D at all temporal scales. Though GMI can reproduce observed TCWV variations better than the INSAT-3D, the large biases of both the data sets indicate errors in the magnitude. Seasonal and monthly comparisons at two locations in the southeast peninsular India region show large correlations and small bias in the northeast and small correlations and large biases in southwest monsoon months. Southeast peninsular India receives a significant amount of rainfall in the northeast monsoon, and large TCWV correlations indicate both the algorithms removing cloud pixels with high accuracy. Therefore, the errors in the TCWV are attributed to the estimated radiances at different spectral channels. The spatiotemporal variations of TCWV correlations and bias of INSAT-3D indicate the need for improving the data quality by validating the estimated radiances at different spectral channels and, in turn, the retrieved TCWV over various regions at different temporal scales.

Diversity in Expression Biases of Lineage-Specific Genes During Development and Anhydrobiosis Among Tardigrade Species.

Lineage-specific genes can contribute to the emergence and evolution of novel traits and adaptations. Tardigrades are animals that have adapted to tolerate extreme conditions by undergoing a form of cryptobiosis called anhydrobiosis, a physical transformation to an inactive desiccated state. While studies to understand the genetics underlying the interspecies diversity in anhydrobiotic transitions have identified tardigrade-specific genes and family expansions involved in this process, the contributions of species-specific genes to the variation in tardigrade development and cryptobiosis are less clear. We used previously published transcriptomes throughout development and anhydrobiosis (5 embryonic stages, 7 juvenile stages, active adults, and tun adults) to assess the transcriptional biases of different classes of genes between 2 tardigrade species, Hypsibius exemplaris and Ramazzottius varieornatus. We also used the transcriptomes of 2 other tardigrades, Echiniscoides sigismundi and Richtersius coronifer, and data from 3 non-tardigrade species (Adenita vaga, Drosophila melanogaster, and Caenorhabditis elegans) to help identify lineage-specific genes. We found that lineage-specific genes have generally low and narrow expression but are enriched among biased genes in different stages of development depending on the species. Biased genes tend to be specific to early and late development, but there is little overlap in functional enrichment of biased genes between species. Gene expansions in the 2 tardigrades also involve families with different functions despite homologous genes being expressed during anhydrobiosis in both species. Our results demonstrate the interspecific variation in transcriptional contributions and biases of lineage-specific genes during development and anhydrobiosis in 2 tardigrades.