Transition Bias Research Articles

C→U transition biases in SARS-CoV-2: still rampant 4 years from the start of the COVID-19 pandemic.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the pandemic and post-pandemic periods has shown a remarkable capacity to adapt and evade human immune responses and increase its human-to-human transmissibility. The genome of SARS-CoV-2 is also increasingly scarred by the effects of multiple C→U mutations from host genome editing as a cellular defense mechanism akin to restriction factors for retroviruses. Through the analysis of large data sets of SARS-CoV-2 isolate sequences collected throughout the pandemic period and beyond, we show that C→U transitions have driven a base compositional change over time amounting to a net loss of C bases and accumulation of U's at a rate of approximately 0.2%-0.25%/decade. Most C→U substitutions occurred in the absence of the preferred upstream-base context or targeting of unpaired RNA bases previously associated with the host RNA editing protein, APOBEC 3A. The analyses provide a series of testable hypotheses that can be experimentally investigated in the future.

Microstructure, first-order magnetostructural transition, magnetocaloric properties and exchange bias effect in Ni45−xBixMn44Sn11 alloys

Microstructure, first-order magnetostructural transition, magnetocaloric properties and exchange bias effect in Ni45−xBixMn44Sn11 alloys

Structural phase transition and tunable exchange bias effect in La1·5Sr0·5CoMnO6 nanoparticles with particle size

The effect of particle size on the crystal structure and magnetic behaviors of the double perovskite oxide La1·5Sr0·5CoMnO6 was systematically investigated. As the particle size increases from 45 nm to 308 nm, the crystal structure undergoes a gradual transformation from a cubic phase with the Pm-3m space group to the rhombohedral phase (R-3c). The magnetic data reveals that the Griffiths phase (GP) can be induced and enhanced by an increase in particle size. Importantly, the modulation of the conventional and spontaneous exchange bias (EB) of the system was effectively achieved by crystal growth, i.e., a monotonically increased EB field with an increase of particle size. This phenomenon can be attributed to the enhancement in the antiferromagnetic (AFM) interfacial anisotropy based on the Meiklejohn-Bean model. Our results provide evidence that crystal growth plays a crucial role in modulating the EB effect in double perovskite.

Augmenting tomato functional genomics with a genome-wide induced genetic variation resource.

Induced mutations accelerate crop improvement by providing novel disease resistance and yield alleles. However, the alleles with no perceptible phenotype but have an altered function remain hidden in mutagenized plants. The whole-genome sequencing (WGS) of mutagenized individuals uncovers the complete spectrum of mutations in the genome. Genome-wide induced mutation resources can improve the targeted breeding of tomatoes and facilitate functional genomics. In this study, we sequenced 132 doubly ethyl methanesulfonate (EMS)-mutagenized lines of tomato and detected approximately 41 million novel mutations and 5.5 million short InDels not present in the parental cultivar. Approximately 97% of the genome had mutations, including the genes, promoters, UTRs, and introns. More than one-third of genes in the mutagenized population had one or more deleterious mutations predicted by Sorting Intolerant From Tolerant (SIFT). Nearly one-fourth of deleterious genes mapped on tomato metabolic pathways modulate multiple pathway steps. In addition to the reported GC>AT transition bias for EMS, our population also had a substantial number of AT>GC transitions. Comparing mutation frequency among synonymous codons revealed that the most preferred codon is the least mutagenic toward EMS. The validation of a potato leaf-like mutation, reduction in carotenoids in ζ-carotene isomerase mutant fruits, and chloroplast relocation loss in phototropin1 mutant validated the mutation discovery pipeline. Our database makes a large repertoire of mutations accessible to functional genomics studies and breeding of tomatoes.

Cryptic Speciation and Characteristics of the Transition Bias Following an Example of the cytb Gene in Palearctic Mammals

A study of taxonomic differentiation and transition bias of the cytb gene, focusing on the early stages of speciation, was carried out in 15 subfamilies/families of five orders of Palearctic mammals. It was confirmed that the genetic differentiation among taxa of small and large mammals is shifted by the same taxonomic level, in which connection the period of cryptic speciation of Micromammalia (semi- and allospecific levels) corresponds to the divergence of type species in their genus within Macromammalia. In all cases, both transition bias and its evolutionary compensation took place. The novelty of the study also lies in the proof that the alignment of the transitions and transversion rates in evolutionary lineages has the pattern of a phase transition, and the frequency of transversions in short-cycle species of the orders Insectivora and Rodentia is higher than in long-cycle orders Artiodactyla, Carnivora and Chiroptera while with relative equality of transitions. The latter circumstance might be associated with the traits of metabolism and determines the characteristics of the molecular evolution of mammalian groups with short and long life cycles.

Autonomous behaviour and the limits of human volition

Humans and some other animals can autonomously generate action choices that contribute to solving complex problems. However, experimental investigations of the cognitive bases of human autonomy are challenging, because experimental paradigms typically constrain behaviour using controlled contexts, and elicit behaviour by external triggers. In contrast, autonomy and freedom imply unconstrained behaviour initiated by endogenous triggers. Here we propose a new theoretical construct of adaptive autonomy, meaning the capacity to make behavioural choices that are free from constraints of both immediate external triggers and of routine response patterns, but nevertheless show appropriate coordination with the environment. Participants (N = 152) played a competitive game in which they had to choose the right time to act, in the face of an opponent who punished (in separate blocks) either choice biases (such as always responding early), sequential patterns of action timing across trials (such as early, late, early, late…), or predictable action-outcome dependence (such as win-stay, lose-shift). Adaptive autonomy was quantified as the ability to maintain performance when each of these influences on action selection was punished. We found that participants could become free from habitual choices regarding when to act and could also become free from sequential action patterns. However, they were not able to free themselves from influences of action-outcome dependence, even when these resulted in poor performance. These results point to a new concept of autonomous behaviour as flexible adaptation of voluntary action choices in a way that avoids stereotypy. In a sequential analysis, we also demonstrated that participants increased their reliance on belief learning in which they attempt to understand the competitor's beliefs and intentions, when transition bias and reinforcement bias were punished. Taken together, our study points to a cognitive mechanism of adaptive autonomy in which competitive interactions with other agents could promote both social cognition and volition in the form of non-stereotyped action choices.

Transition Bias and Its Compensation in the Evolutionary Lineage of the Subfamily Murinae (Rodentia): Analysis of Nuclear and Mitochondrial DNA Markers

Transition Bias and Its Compensation in the Evolutionary Lineage of the Subfamily Murinae (Rodentia): Analysis of Nuclear and Mitochondrial DNA Markers

Spectroscopic characterization of the quantum linear-zigzag transition in trapped ions

While engineered quantum systems are a general route to the manipulation of multipartite quantum states, access in a physical system to a continuous quantum phase transition under sufficient control offers the possibility of an intrinsic source of entangled states. To this end we realize the quantum version of the linear-zigzag structural transition for arrays of up to five ground state-cooled ions held in a linear Paul trap and we demonstrate several of the control requirements towards entangled-state interferometry near the critical point. Using in situ spectroscopy we probe the energy level structure and occupation of the soft mode associated with the structural transition, and show a stable critical point and majority ground state occupation crossing the transition. We resolve biases arising from trap electrode asymmetries that change the nature of the transition, show that they can be suppressed by varying the ion number, and demonstrate control of the transition bias using optical dipole forces.

Green transition and gender bias: An analysis of renewable energy generation companies in Latin America

This study analyzes how the energy transition might change gender bias in power-generating industries. We employ a sample of 102 renewable energy generation companies from six countries in Latin America and the Caribbean: Bolivia, Chile, Costa Rica, Panama, Mexico, and Uruguay. The analysis shows that renewable generation companies with the highest relative efficiency in the labor-capital ratio are those with the highest participation of women. In addition, the results show that renewable companies are incrementing recruitment of women in energy generation; however, their participation is still lower than the sectorial average. Considering the companies' size, bigger renewables companies tend to hire more women, but those women occupy mostly non-technical positions. In addition, women's participation decreases in positions requiring higher education. Women represent 38 % of STEM employees, 54 % of non-STEM employees, and 55 % of non-qualified employees among the total of people employed in generation companies. This trend is even more acute for renewable energy generation companies, where women represent 36 % of STEM employees, 39 % of non-STEM employees, and 48 % of non-qualified employees. Concerning the role of women in decision-making roles within energy companies, wide gender gaps exist in executive and management positions; the proportion of females in the boardroom and in management roles for renewables generation companies was 24 % and 22 %, respectively. Furthermore, 68 % of surveyed companies did not have a gender policy in place. This study confirms that a change in technology alone does not generate qualitative changes in the labor market from a gender perspective.

Validation of Simplified Level 2 Prototype Processor Sentinel-2 fraction of canopy cover, fraction of absorbed photosynthetically active radiation and leaf area index products over North American forests

Canopy biophysical variables such as the fraction of canopy cover (fCOVER), fraction of absorbed photosynthetically active radiation (fAPAR), and leaf area index (LAI) are widely used for ecosystem modelling and monitoring. The Sentinel-2 mission was designed for systematic global mapping of these variables at 20 m resolution using imagery from the MultiSpectral Instrument. The Simplified Level 2 Prototype Processor (SL2P) is available as a baseline mapping solution. Previous validation over limited sites indicates that SL2P generally satisfies user requirements for all three variables over crops, but underestimates LAI over forests. In this study, Sentinel-2 fAPAR, fCOVER, and LAI products, from SL2P, were validated over 281 sites representative of most North American forest ecozones and also compared to Moderate Resolution Imaging Spectrometer (MODIS) and Copernicus Global Land Service (CGLS) products. In addition to meeting the Committee on Earth Observation Satellites Stage 3 validation requirements for these areas, our study also explores the relationship between bias in SL2P products and canopy clumping and provides empirical bias correction functions for each variable.SL2P was implemented within the Landscape Evolution and Forecasting Toolbox in Google Earth Engine both for efficiency and due to bugs in the Sentinel Application Platform implementation. SL2P was found to underestimate LAI by 20% to 50% over forests with LAI > 2; in agreement with other studies and with comparisons to MODIS and CGLS products. SL2P bias for fCOVER and fAPAR transitions from ∼0.1 at low values to ∼ − 0.1 at high values. Precision error, at one standard deviation, was ∼0.5 for LAI and slightly less than ∼0.1 for fCOVER and fAPAR. Total uncertainty was dominated by bias for LAI and was slightly greater than precision error for fCOVER and fAPAR. Target user requirements were satisfied for 51% of LAI, 37% of fCOVER and 31% of fAPAR comparisons to in-situ measurements. For all variables, accuracy exhibited weak to moderate linear relationships to clumping (r2 ≤0.52), but scatter plots indicated larger negative LAI biases over northern latitude sites where canopies exhibited greater clumping. With the exception of evergreen broadleaf forests, empirical bias correction using in-situ data reduced accuracy error by 40% for fCOVER, 57% for fAPAR and, 92% for LAI and increased the agreement rate with uncertainty requirements by up to 8%. Users of SL2P LAI over forests are recommended to apply bias correction or consider recalibrating SL2P with spatially heterogenous radiative transfer model simulations.

Enhancing network lifespan in wireless sensor networks using deep learning based Graph Neural Network

Inadequate energy of sensors is one of the most significant challenges in the development of a reliable wireless sensor network (WSN) that can withstand the demands of growing WSN applications. Implementing a sleep-wake scheduling scheme while assigning data collection and sensing chores to a dominant group of awake sensors while all other nodes are in a sleep state seems to be a potential way for preserving the energy of these sensor nodes. When the starting energy of the nodes changes from one node to another, this issue becomes more difficult to solve. The notion of a dominant set-in graph has been used in a variety of situations. The search for the smallest dominant set in a big graph might be time-consuming. Specifically, we address two issues: first, identifying the smallest possible dominant set, and second, extending the network lifespan by saving the energy of the sensors. To overcome the first problem, we design and develop a deep learning-based Graph Neural Network (DL-GNN). The GNN training method and back-propagation approach were used to train a GNN consisting of three networks such as transition network, bias network, and output network, to determine the minimal dominant set in the created graph. As a second step, we proposed a hybrid fixed-variant search (HFVS) method that considers minimal dominant sets as input and improves overall network lifespan by swapping nodes of minimal dominating sets. We prepared simulated networks with various network configurations and modeled different WSNs as undirected graphs. To get better convergence, the different values of state vector dimensions of the input vectors are investigated. When the state vector dimension is 3 or 4, minimum dominant set is recognized with high accuracy. The paper also presents comparative analyses between the proposed HFVS algorithm and other existing algorithms for extending network lifespan and discusses the trade-offs that exist between them. Lifespan of wireless sensor network, which is based on the dominant set method, is greatly increased by the techniques we have proposed.

HexSE: Simulating evolution in overlapping reading frames.

Gene overlap occurs when two or more genes are encoded by the same nucleotides. This phenomenon is found in all taxonomic domains, but is particularly common in viruses, where it may provide a mechanism to increase the information content of compact genomes. The presence of overlapping reading frames (OvRFs) can skew estimates of selection based on the rates of non-synonymous and synonymous substitutions, since a substitution that is synonymous in one reading frame may be non-synonymous in another and vice versa. To understand the impact of OvRFs on molecular evolution, we implemented a versatile simulation model of nucleotide sequence evolution along a phylogeny with any distribution of open reading frames in linear or circular genomes. We use a custom data structure to track the substitution rates at every nucleotide site, which is determined by the stationary nucleotide frequencies, transition bias and the distribution of selection biases (dN/dS) in the respective reading frames. Our simulation model is implemented in the Python scripting language. All source code is released under the GNU General Public License version 3 and are available at https://github.com/PoonLab/HexSE.

Manipulation of the Martensitic Transformation and Exchange Bias Effect in the Ni45Co5Mn37In13 Ferromagnetic Shape Memory Alloy Films

The martensitic phase transition and exchange bias effect of the Ni-Mn-based ferromagnetic shape memory alloys (FSMAs) Ni45Co5Mn37In13 (Ni-Co-Mn-In) films are investigated in this paper. The martensitic transformation properties of the Ni-Co-Mn-In alloy target material are manipulated by the process of electric arc melting, melt-fast quenching, and high-temperature thermal pressure. The Ni-Co-Mn-In alloy films with martensite phase transition characteristics are obtained by adjusting deposition parameters on the (001) MgO substrate, which shows a significant exchange bias (EB) effect at different temperatures. With increasing sputtering power and time, the film thickness increases, resulting in a gradual relaxation of the constraints at the interface between the film and the substrate (the interfacial strain decreases as the increase of thin film thickness), which promotes the martensite phase transition. Between zero-field cooling (ZFC) and field-cooled (FC) curve obvious division zone, the decrease of exchange bias field (HEB) and coercive force field (Hc) with an increase in test temperature is due to ferromagnetic (FM) interaction begins to dominate, resulting in a reduction of antiferromagnetic (AFM) anisotropy at the interface. The maximal HEB and Hc reach ~465.7 Oe and ~306.9 Oe at 5 K, respectively. The manipulation of the martensitic transformation and EB effect of the Ni-Co-Mn-In alloy films demonstrates potential application in the field of information and spintronics.

Strand-Specific Patterns of Codon Usage Bias Across Cressdnaviricota

The rapidly expanding phylum Cressdnaviricota contains circular, Rep-encoding single-stranded (CRESS) DNA viruses that are organized within seven established families, but many CRESS DNA virus sequences are not taxonomically defined. We hypothesized that genes in CRESS DNA virus ambisense genomes exhibit strand-specific signatures due to a cytosine to thymine transition bias that can help determine the orientation of the genome: which strand is packaged and is in the “virion sense”. To identify broad strand-specific patterns across genera, we performed compositional analyses of codon usage across the two major opposite sense open reading frames of 712 reference viruses. Additionally, we developed a statistical test to identify relative codon overrepresentation between ambisense sequence pairs for each classified virus exemplar and an additional 137 unclassified CRESS DNA viruses. Codons clustered by the identity of their third-position nucleotide, displaying both strand- and genus-specific patterns across Cressdnaviricota. Roughly 70% of virion-sense sequences have a relative overrepresentation of thymine-ending codons while ~80% of anti-sense sequences display a relative overrepresentation of adenine-ending codons (corresponding to a relative overrepresentation of thymine in these genes as packaged). Thirteen of the 137 unclassified viruses show strong evidence of having the rarer circovirus-like genome orientation, and likely represent novel genera or families within Cressdnaviricota. Given the strong strand-specific patterns of relative codon overrepresentation, the results suggest that the relative codon overrepresentation test can serve as a tool to help corroborate the genome organization of unclassified CRESS DNA viruses.

Spin Reorientation Transition and Exchange Bias in Hard/Soft Tb–Co/FeNi Films

Magnetization studies were carried out for Tb–Co thin films and Tb–Co/FeNi bilayers, prepared by magnetron sputtering technique. The composition of the Tb–Co films varied in the range of 19–24 at.%. All Tb–Co films were found to have perpendicular magnetic anisotropy in a wide temperature range. In addition, for some Tb–Co films, a spin reorientation transition was observed in the investigated temperature range. An analysis of the obtained results suggests that, in the course of deposition of the FeNi layer onto the Tb–Co layer, an interlayer magnetic boundary is formed, and its parameters depend on the composition of the Tb–Co layer. The magnetic structure peculiarities of this boundary determine the value of the exchange bias in Tb–Co/FeNi bilayers and its temperature dependence.

Understanding population structure and detection of QTLs for curding-related traits in Indian cauliflower by genotyping by sequencing analysis.

Curd initiation and development are complex traits and highly responsive for different temperature ranges in cauliflower. The present study was aimed to identify QTLs for eight traits associated with curding behaviour in diverse germplasm of Indian cauliflower. For this, 92 genotypes of cauliflower and 2 each of tropical broccoli and cabbage were genotyped through genotyping by sequencing (GBS). It generated ≈302 million reads (9.1226E + 10bp) and identified 35,381 SNPs, maximum from chromosome 3 (4735) with a mean value of 3981.1 SNPs. Ts/Tv ratio was 1.74, suggesting transition bias. STRUCTURE analysis revealed delta value of K = 4 and four subpopulations and prominence of population admixture. In total, 121 significant SNPs were detected for eight traits, 38 for Delhi (North Indian plain) and 83 for Barapani (North-East India). Twelve QTLs were detected for traits associated with regulation of curd formation and development, five of which were for marketable curd length, curd width, days to 50% curd harvest and marketable curd weight from Delhi region and seven for curd length, curd width, days to 50% curd harvest, gross plant weight, leaf length, marketable/net curd weight and number of leaves per plant for Barapani area of North East India. The SNPs identified will be useful for development of markers for curding-related traits and their use in breeding varieties with wider curding plasticity.

Extensive C->U transition biases in the genomes of a wide range of mammalian RNA viruses; potential associations with transcriptional mutations, damage- or host-mediated editing of viral RNA.

The rapid evolution of RNA viruses has been long considered to result from a combination of high copying error frequencies during RNA replication, short generation times and the consequent extensive fixation of neutral or adaptive changes over short periods. While both the identities and sites of mutations are typically modelled as being random, recent investigations of sequence diversity of SARS coronavirus 2 (SARS-CoV-2) have identified a preponderance of C->U transitions, proposed to be driven by an APOBEC-like RNA editing process. The current study investigated whether this phenomenon could be observed in datasets of other RNA viruses. Using a 5% divergence filter to infer directionality, 18 from 36 datasets of aligned coding region sequences from a diverse range of mammalian RNA viruses (including Picornaviridae, Flaviviridae, Matonaviridae, Caliciviridae and Coronaviridae) showed a >2-fold base composition normalised excess of C->U transitions compared to U->C (range 2.1x–7.5x), with a consistently observed favoured 5’ U upstream context. The presence of genome scale RNA secondary structure (GORS) was the only other genomic or structural parameter significantly associated with C->U/U->C transition asymmetries by multivariable analysis (ANOVA), potentially reflecting RNA structure dependence of sites targeted for C->U mutations. Using the association index metric, C->U changes were specifically over-represented at phylogenetically uninformative sites, potentially paralleling extensive homoplasy of this transition reported in SARS-CoV-2. Although mechanisms remain to be functionally characterised, excess C->U substitutions accounted for 11–14% of standing sequence variability of structured viruses and may therefore represent a potent driver of their sequence diversification and longer-term evolution.

Strain Control of Phase Transition and Exchange Bias in Flexible Heusler Alloy Thin Films.

The practical applications for the distinctive functions of metamagnetic Heusler alloys, such as magnetic shape memory effect, various caloric effects, etc., strongly depend on the phase transition temperatures. Here, flexible Heusler alloy Ni-Mn-Sn films have been deposited on mica substrates by pulsed laser deposition with a Ti buffer layer. Clear ferromagnetic (FM) transition followed by the martensitic transformation at around room temperature and exchange bias (EB) with a blocking temperature of 70 K are observed. Under the application of both tensile and compressive strains by bending the mica substrates, all the characteristic temperatures of Ni-Mn-Sn films, including the FM transition temperature, martensitic transformation temperature, and blocking temperature of EB, are significantly increased by about 10 K. Furthermore, EB field and coercivity are both strongly strengthened, which is mainly caused by the simultaneous enhancement of FM and anti-FM Mn-Mn coupling because of their shortened separations by strain and verified by the Monte Carlo simulation results. The strain controlling for structural and magnetic properties provides efficient manipulation for Heusler alloy-based magnetic devices.

Martensitic Transition, Magnetic, Microstructural and Exchange Bias Properties of Melt Spun Ribbons of Mn-Ni-Sn Shape Memory Heusler Alloy

In the present report, we have studied the structural, microstructural, magnetic, exchange bias (EB) properties and magnetoresistance (MR) in Mn rich (Mn at. ∼50%) Mn50Ni50−xSnx (x = 10) shape memory Heusler alloy ribbons, prepared using the melt spinning method. These ribbons were found to exhibit a first order structural (i.e., martensitic) transition at around 205 K from the high temperature austenite to the low temperature martensite phase. The martensitic transition occurs at comparatively lower temperatures in these ribbons than in the same bulk alloy. Curie temperature of the austenite phase (TCA) is found to be larger i.e., around room temperature than that of bulk alloy. A significant EB field (HEB) of around 960 Oe has been observed at 2 K for these ribbons, which is found to be comparable to that reported for other Heusler systems. The presence of the EB effect in these ribbons is attributed to the coexistence of FM/AFM exchange interactions in the martensite phase. They are also found to show a maximum negative MR of around 12% near the martensitic transition, for 50 kOe field change. Investigation of DC magnetization, AC susceptibility measurements and the observation of training effect (i.e., characteristic feature of EB) strongly corroborates with the coexistence of FM/AFM exchange interactions in the martensite phase of these ribbons, which results in the large EB. The effects of temperature and magnetic field on the EB properties and MR have also been studied here.

Macroevolution of Flower Color Patterning: Biased Transition Rates and Correlated Evolution with Flower Size.

Floral pigmentation patterns can both mediate plant-pollinator interactions and modify the abiotic environment of reproductive structures. To date, there have been no inquiries into the rate and directionality of macroevolutionary transitions between patterned and non-patterned petals despite their ecological importance and ubiquity across angiosperms. Petals in the Potentilleae tribe (Rosaceae) display color patterns in the ultraviolet (UV) and human-visible spectrum, or can be uniform in color (i.e., patternless). Using a phylogeny of Potentilleae, I test whether evolutionary transition rates between patterned and non-patterned petals are biased in either direction. I then examine whether UV and human-visible floral patterns are phylogenetically correlated and test the prediction that color patterns will evolve in concert with larger flowers if they function as guides to orient pollinators to floral rewards. I found that transition rates were biased toward petals that were uniform in color. Transition rates from patterned to uniformly colored petals were two and six times higher than the reverse for UV and human-visible pattern, respectively. The presence of UV and human-visible pattern evolved independently from one another. However, the evolution of human-visible pattern was associated with the evolution of larger flowers but the evolution of UV pattern was correlated with the evolution of smaller flowers. I posit that the transition bias toward non-patterned flowers may reflect developmental constraints on spatial regulation of pigments required to produce floral color patterning. The correlated evolution of larger flowers and human-visible pigmentation patterns support the hypothesis that nectar or pollen guides are more likely to evolve in larger-flowered species. This work provides insight into how transition rate bias and trait correlations can shape phylogenetic patterns of floral color pattern diversity.