Miracle-dz/UniFAR-FTUs huggingface dataset:
A new codon adaptation metric predicts vertebrate body size and tendency to protein disorder

The nearly neutral theory of molecular evolution posits variation among species in the effectiveness of selection. In an idealized model, the census population size determines both this minimum magnitude of the selection coefficient required for deleterious variants to be reliably purged, and the amount of neutral diversity. Empirically, an “effective population size” is often estimated from the amount of putatively neutral genetic diversity, and is assumed to also capture a species’ effectiveness of selection. The degree to which selection maintains preferred codons has the potential to more directly quantify the effectiveness of selection. However, past metrics that compare codon bias across species are confounded by among-species variation in %GC content and/or amino acid composition. Here we propose a new Codon Adaptation Index of Species (CAIS) that corrects for both confounders. Unlike previous metrics of codon bias, CAIS yields the expected relationship with adult vertebrate body mass. We demonstrate the use of CAIS correlations to show that the protein domains of more highly adapted vertebrate species evolve higher intrinsic structural disorder.
Clustered synapses develop in distinct dendritic domains in visual cortex before eye opening

Synaptic inputs to cortical neurons are highly structured in adult sensory systems, such that neighboring synapses along dendrites are activated by similar stimuli. This organization of synaptic inputs, called synaptic clustering, is required for high-fidelity signal processing, and clustered synapses can already be observed before eye opening. However, how clustered inputs emerge during development is unknown. Here, we employed concurrent in vivo whole-cell patch clamp and dendritic calcium imaging to map spontaneous synaptic inputs to dendrites of layer 2/3 neurons in the mouse primary visual cortex during the second postnatal week until eye opening. We find that the number of functional synapses and the frequency of transmission events increase several fold during this developmental period. At the beginning of the second postnatal week, synapses assemble specifically in confined dendritic segments, whereas other segments are devoid of synapses. By the end of the second postnatal week, just before eye-opening, dendrites are almost entirely covered by domains of co-active synapses. Finally, co-activity with their neighbor synapses correlates with synaptic stabilization and potentiation. Thus, clustered synapses form in distinct functional domains presumably to equip dendrites with computational modules for high-capacity sensory processing when the eyes open.
A Wide-Field, Broadband Imaging Survey of Butcher-Oemler Cluster Cl 0024+1654: The Catalog

Wide-field (20′ × 20′) UBVI images of intermediate-redshift (z = 0.39), Butcher-Oemler cluster Cl 0024+1654 have been obtained. These data probe the rest-frame mid-UV properties over a much larger area than previous studies of Cl 0024+1654. Using these data, a multicolor catalog of nonstellar objects, assumed to be galaxies, has been constructed and analyzed. Using statistical arguments, the observed galaxy sample is separated into field and cluster populations. The basic photometric properties of these populations are presented and discussed. The "dropout" objects (i.e., objects undetected in one or more photometric bands) in our catalog are also discussed. A description of the final UBVI images, as well as the object catalog, is provided in an appendix. In a second appendix the use of SExtractor in crowded fields, such as the core of Cl 0024+1654, is discussed. The specific issues of the mid-UV properties of red envelope cluster galaxies, as well as the possible detection of a faint blue cluster population, are discussed in a forthcoming companion paper by Silva, Alexov, & Pierce.
Host selection has stronger impact on leaf microbiome assembly compared to land-management practices

Plant microbiome contribute directly to plant health and productivity but mechanisms that underpin plant microbiome assembly in different compartments (e.g. root, leaf) are not fully understood. Identifying environmental and management factors that affect plant microbiome assembly is important to advance understanding of fundamental ecological processes and harnessing microbiome for improved primary productivity and environmental sustainability. Irrigation and fertilization are two common management practices in Australian tree plantations, but little is known about the effects of these treatments on soil, plant host, and their microbiome. Here, we investigated the impact of a decade long irrigation, fertilization, and their combined application, on soil, plant traits and microbiome of a Eucalyptus saligna plantation at the Hawkesbury Forest Experiment, Western Sydney University, Richmond, NSW. Microbial profiling of bulk soil, rhizosphere, root, and leaves was performed using amplicon sequencing 16S rDNA and ITS markers for bacteria and fungi, respectively, along with measurements of soil properties and plant traits. The results indicated that both management practices affected soil properties and soil and root microbiome significantly. Irrigation increased but fertilizer treatment reduced microbial alpha diversity. However, neither irrigation nor fertilizer treatment significantly impacted the leaf microbiome. Our findings imply that management practices impact soil edaphic factors, which in turn influence the below ground microbiome (soil and root). In addition, the leaf microbiome was distinct from soil and root microbiome, and a source tracker analysis suggested root and bulk soils only contributed to 53% and 10% OTUs of the leaf bacterial community, suggesting strong and sequential host selection of the leaf microbiome. In addition, management practices had limited impact on leaf traits and, consequently, the leaf microbiome maintained its distinct composition. These findings provide mechanistic evidence for ecological processes that drive plant microbiome assembly and indicate that host selection plays a more important role than management practices on leaf microbiome assembly.
Genomic repeat landscape evolution across the teleost fish lineages

Repetitive DNA make up a considerable fraction of most eukaryotic genomes. In fish, transposable element (TE) activity have coincided with rapid species diversification. Here, we annotated the repetitive content in 100 genome assemblies, covering the major branches of the diverse lineage of teleost fish. We investigated if TE content correlates with family level net diversification rates and found support for a weak negative correlation. Further, we found that TE content, the degree of parental care and short tandem repeat (STR) content contributed to genome size variability. In contrast to TEs, STR content showed a negative relationship with genome size. STR content did not correlate with TE content, which implies independent evolutionary paths. Last, marine and freshwater fish have large differences in STR content. The most extreme propagation was found in the genomes of codfish species and Atlantic herring. Such a high density of STRs is likely to increase the mutational load, which we propose could be counterbalanced by high fecundity as seen in codfishes and herring.
Scrutinizing the Feasibility of Macroscopic Quantum Coherence in the Brain: A Field-Theoretical Model of Cortical Dynamics

The neural activity patterns associated with advanced cognitive processes are characterized by a high degree of collective organization, which raises the question of whether macroscopic quantum phenomena play a significant role in cortical dynamics. In order to pursue this question and scrutinize the feasibility of macroscopic quantum coherence in the brain, a model is developed regarding the functioning of microcolumns, which are the basic functional units of the cortex. This model assumes that the operating principle of a microcolumn relies on the interaction of a pool of neurotransmitter (glutamate) molecules with the vacuum fluctuations of the electromagnetic field, termed zero-point field (ZPF). Quantitative calculations reveal that the coupling strength of the glutamate pool to the resonant ZPF modes lies in the critical regime in which the criterion for the initiation of a phase transition is fulfilled, driving the ensemble of initially independent molecules toward a coherent state and resulting in the formation of a coherence domain that extends across the full width of a microcolumn. The formation of a coherence domain turns out to be an energetically favored state shielded by a considerable energy gap that protects the collective state against thermal perturbations and entails decoherence being greatly slowed down. These findings suggest that under the special conditions encountered in cortical microcolumns the emergence of macroscopic quantum phenomena is feasible. This conclusion is further corroborated by the insight that the presence of a coherence domain gives rise to downstream effects which may be crucial for the cortical communication and the formation of large-scale activity patterns. Taken together, the presented model sheds new light on the fundamental mechanism underlying cortical dynamics and suggests that long-range synchronization in the brain results from a bottom-up orchestration process involving the ZPF.
The eccDNA mediated spread and rapid evolution of herbicide resistance in pigweed interspecific hybrids

Extrachromosomal circular DNAs (eccDNAs) are found in many eukaryotic organisms. The eccDNA-powered copy number variation plays diverse roles from oncogenesis in humans to herbicide resistance in crop weeds. Here we report interspecific eccDNA flow and its dynamic behavior in soma cells of natural populations and F1 hybrids of Amaranthus sp. The glyphosate resistance (GR) trait is controlled by eccDNA-based amplification harboring the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene (EPSPS-eccDNA), the molecular target of glyphosate. We documented pollen-mediated transfer of eccDNA in experimental hybrids between GS A. tuberculatus x GR A. palmeri. Experimental hybridization and fluorescence in situ hybridization (FISH) analysis revealed that the EPSPS-eccDNA present in A. spinosus was derived from GR A. palmeri by natural hybridization. FISH analysis also revealed random chromosome anchoring and massive EPSPS-eccDNA copy number variation in soma cells of weedy hybrids. The results suggest that eccDNAs are inheritable across compatible species contributing to genome plasticity and rapid adaptive evolution.
Multimodal neural correlates of childhood psychopathology

Complex structural and functional changes occurring in typical and atypical development necessitate multidimensional approaches to better understand the risk of developing psychopathology. Here, we simultaneously examined structural and functional brain network patterns in relation to dimensions of psychopathology in the Adolescent Brain Cognitive Development dataset. Several components were identified, recapitulating the psychopathology hierarchy, with the general psychopathology (p) factor explaining most covariance with multimodal imaging features, while the internalizing, externalizing, and neurodevelopmental dimensions were each associated with distinct morphological and functional connectivity signatures. Connectivity signatures associated with the p factor and neurodevelopmental dimensions followed the sensory-to-transmodal axis of cortical organization, which is related to the emergence of complex cognition and risk for psychopathology. Results were consistent in two separate data subsamples, supporting generalizability, and robust to variations in analytical parameters. Our findings help in better understanding biological mechanisms underpinning dimensions of psychopathology, and could provide brain-based vulnerability markers.
Patient and cell-type specific hiPSC-modeling of a truncating titin variant associated with atrial fibrillation

Background Protein truncating mutations in the titin gene are associated with increased risk of atrial fibrillation (AF). However, little is known regarding the underlying pathophysiology. Methods We identified a heterozygous titin truncating variant in a patient with unexplained early-onset AF using whole exome sequencing. We used atrial and ventricular patient induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs), CRISPR/Cas9 genetic correction, and engineered heart tissue (EHT) constructs to evaluate the impact of the titin truncating variant on electrophysiology, sarcomere structure, contractility, and gene expression. Results We generated atrial and ventricular iPSC-CMs from the AF patient with the titin truncating variant and a CRISPR/Cas9 genome corrected isogenic control. We demonstrate that the titin truncating variant increases susceptibility to pacing-induced arrhythmia (prevalence of arrhythmogenic phenotypes, 85.7% versus 14.2%; P = 0.03), promotes sarcomere disorganization (mean ± SEM, 66.3 ± 6.8% versus 88.0 ± 2.9%; P = 0.04) in atrial iPSC-CMs, and reduces contractile force (0.013 ± 0.003 mN versus 0.027 ± 0.004 mN; P < 0.01) in atrial EHTs compared to isogenic controls. In ventricular iPSC-CMs, this variant led to altered electrophysiology (90.0% versus 33.3%; P = 0.02) and sarcomere organization (62.0 ± 3.9% versus 82.9 ± 2.9%; P < 0.01) with no change in EHT contractility compared to isogenic controls. RNA-sequencing revealed an upregulation of cell adhesion and extracellular matrix genes in the presence of the titin truncating variant for both atrial and ventricular EHTs. Conclusions In a patient with early-onset unexplained AF and normal ventricular function, iPSC-CMs with a titin truncating variant showed structural and electrophysiological abnormalities in both atrial and ventricular preparations, while only atrial EHTs demonstrated reduced contractility. Whole transcriptome sequencing showed upregulation of genes involved in cell-cell and cell-matrix interactions in both atrial and ventricular EHTs. Together, these findings suggest titin truncating variants promote the development of AF through remodeling of atrial cardiac tissue and provide insight into the chamber-specific effects of titin truncating variants.
The Source, Size and Chemical Composition of the Winter Arctic Tropospheric Aerosol Layer Observed by Lidar at Eureka, Canada

During the winter seasons from 1993-94 to 1998-99 at Eureka (80.0°N, 86.0°W) in the Canadian high arctic, we have observed tropospheric aerosol layers by using a Mie-scattering-polarization lidar system and we have investigated lidar parameters (Mie backscattering coefficients, aerosol depolarization ratios, and Angstrom exponents) of the layers. We calculated isentropic back trajectories in order to investigate the source regions of these layers. We also estimated the size of the particles in the layers by calculating modeled lidar parameters and comparing them with the observed lidar parameters. Daily sampling of aerosol particles was carried out in the late winter of 1998-99. Isentropic back trajectories of the aerosol layer observed over Eureka at different altitudes suggested that the source regions of the aerosol were Eurasia, the northern Pacific and Atlantic Oceans, the Arctic Ocean, and regions near the coast of the Arctic Ocean. The lidar parameters calculated by using the Mie theory and the modeled particle size distribution suggested that, although the Mie backscattering coefficient was determined largely by the number concentration of the accumulation mode particles of diameter 0.2 μm to 0.3 μm, the aerosol depolarization ratio and Angstrom exponent of the aerosol layers were influenced strongly by the number concentration and the geometric mean diameter of the coarse particles. The trajectories, characteristics, and chemical compositions of aerosols suggest that the arctic layers observed by lidar were composed of sulfate aerosol or sea salt.
OBSERVATION OF OPTICALLY-ACTIVE METASTABLE DEFECTS IN UNDOPED GAN EPILAYERS

Optically-active defects of undoped GaN epilayers grown on sapphire by metalorganic chemical vapor epitaxy was investigated with photoluminescence. A new metastable defect emitting blue light was found, besides the well-known yellow luminescence centers. With excitation by the 325 nm He–Cd laser, this metastable defect, at low temperature, exhibits the luminescence fatigue effect with the decay time determined to be about 6 min. When the temperature is increased to room temperature, it recovers its optically-active state. The yellow band emission increases in intensity as the blue band emission decreases in intensity. Analysis shows that this metastable center is a hole trap, and Ga vacancy is its most probable candidate.
Optimum Sample Size for Choosing the Population Having the Smallest Variance (Large Sample Size Results)

Abstract Suppose we have k + 1 populations, each normally distributed. Let σ0 2 be the smallest variance, and a = σ i /σ0. Let p 0(a) be the probability of correct selection when a 1 = a 2 = ···= a . Let W (σ i , σ0) be the cost of selection of the wrong population and C(n) be the cost of sampling n individuals from each population. It is shown under general conditions that the maximum expected loss over all possible variance values is proportional to for large n, and that the maximum occurs for where x* is the value which maximizes x[1 − p 0(x)].
Asymptotic analysis of the modes of wave propagation in a piezoelectric solid cylinder

An asymptotic method due to ’’Achenbach’’ is used to analyze the longitudinal and circumferential modes of wave propagation in a piezoelectric solid circular cylinder of crystal class (6 mm) or ceramics (∞m). Information obtained in this method is useful for the frequency spectrum at long wavelengths. In this method the displacement components, electric potential, and the frequency are expressed as power series of the dimensionless wavenumber, e = 2π× radius/wavelength. Substituting these expansions in the field equations and the boundary conditions, a system of coupled second‐order inhomogeneous ordinary differential equations with radial coordinate as the independent variable is obtained by collecting the terms of same order em. Integration of such systems of differential equations yields the various terms in the series expansions for the above modes and for the whole range of frequencies, when the real valued dimensionless wavenumber is less than unity (0
A compact finite difference method for the solution of the generalized Burgers–Fisher equation

In this article, numerical solutions of the generalized Burgers–Fisher equation are obtained using a compact finite difference method with minimal computational effort. To verify this, a combination of a sixth‐order compact finite difference scheme in space and a low‐storage third‐order total variation diminishing Runge–Kutta scheme in time have been used. The computed results with the use of this technique have been compared with the exact solution to show the accuracy of it. The approximate solutions to the equation have been computed without transforming the equation and without using linearization. Comparisons indicate that there is a very good agreement between the numerical solutions and the exact solutions in terms of accuracy. The present method is seen to be a very good alternative to some existing techniques for realistic problems. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2010
ASYMPTOTIC INFERENCE FOR NONSTATIONARY GARCH

Consistency and asymptotic normality are established for the highly applied quasi-maximum likelihood estimator in the GARCH(1,1) model. Contrary to existing literature we allow the parameters to be in the region where no stationary version of the process exists. This has the important implication that the likelihood-based estimator for the GARCH parameters is consistent and asymptotically normal in the entire parameter region including both stationary and explosive behavior. In particular, there is no “knife edge result like the unit root case” as hypothesized in Lumsdaine (1996, Econometrica 64, 575–596). Anders Rahbek is grateful for support from the Danish Social Sciences Research Council, the Centre for Analytical Finance (CAF), and the EU network DYNSTOCH. Both authors thank the two anonymous referees and the editor for highly valuable and detailed comments that have, we believe, led to a much improved version of the paper, both in terms of the econometric theory and of the presentation.
Frequency-induced polarization bistability in vertical-cavity surface-emitting lasers with orthogonal optical injection

We report theoretically on a pure frequency-induced polarization bistability in a vertical-cavity surface-emitting laser (VCSEL) subject to orthogonal optical injection, i.e., the master laser light polarization is orthogonal to that of the slave VCSEL. As the frequency detuning is scanned from negative to positive values and for a fixed injected power, the VCSEL exhibits two successive and possibly bistable polarization switchings. The first switching (from the slave laser polarization to the injected light polarization) exhibits a bistable region whose width is maximum for a given value of the injected power. Such a dependency of hysteresis width on the injected power is similar to that recently found experimentally by Hong et al.[Electron. Lett. 36, 2019 (2000)]. The bistability accompanying the second switching (from the injected light polarization back to the slave laser free-running polarization) exhibits, however, significantly different features related to the occurrence of optical chaos. Interestingly, the width of the bistable region can be tuned over a large range not only by modifying the injection parameters but also by modifying the device parameters, in particular the VCSEL linewidth enhancement factor.
Limited lookahead policies in supervisory control of discrete event systems

A supervisory control scheme which is based on limited lookahead control policies is proposed, using an online scheme where after the occurrence of an event, the next control action is determined on the basis of an N-step-ahead projection of the behavior of the process (represented as an N-level tree). This procedure then repeats after the execution of the next event. Different attitudes can be adopted to calculate a control action for the given N-level tree in order to resolve uncertainties about the process behavior beyond N steps. Two such attitudes, termed conservative and optimistic. are studied. Results are presented pertaining to monotonicity and convergence properties of the optimistic and conservative N-step policies in terms of N, and comparison of these policies with the optimal offline solution; closed-form expression for the language generated by the N-step conservative policy for prefix-closed legal languages; and lower bounds for N that guarantee that the online scheme performs as well as an offline scheme with complete information. >