Miracle-dz/UniFAR-FTUs huggingface dataset:
Accelerated expansion from cosmological holography

It is shown that holographic cosmology implies an evolving Hubble radius c 1 u RH = −1 + 3m in the presence of a dimensionless matter density m scaled to the closure density 3H 2 /8�G, where c denotes the velocity of light and H and G denote the Hubble parameter and Newton’s constant. It reveals a dynamical dark energy and a sixfold increase in gravitational attraction to matter on the scale of the Hubble acceleration. It reproduces the transition redshift zt ≃ 0.4 to the present epoch of accelerated expansion and is consistent with (q0,(dq/dz)0) of the deceleration parameter q(z) = q0 + (dq/dz)0z observed in Type Ia supernovae.
A predictive model of geosynchronous magnetopause crossings

[1] We have developed a model predicting whether or not the magnetopause crosses geosynchronous orbit at a given location for given solar wind pressure Psw, Bz component of the interplanetary magnetic field (IMF), and geomagnetic conditions characterized by 1 min SYM-H index. The model is based on more than 300 geosynchronous magnetopause crossings (GMCs) and about 6000 min when geosynchronous satellites of GOES and Los Alamos National Laboratory (LANL) series are located in the magnetosheath (so-called MSh intervals) in 1994–2001. Minimizing of the Psw required for GMCs and MSh intervals at various locations, Bz, and SYM-H allows describing both an effect of magnetopause dawn-dusk asymmetry and saturation of Bz influence for very large southward IMF. The asymmetry is strong for large negative Bz and almost disappears when Bz is positive. We found that the larger the amplitude of negative SYM-H, the lower the solar wind pressure required for GMCs. We attribute this effect to a depletion of the dayside magnetic field by a storm time intensification of the cross-tail current. It is also found that the magnitude of threshold for Bz saturation increases with SYM-H index such that for small negative and positive SYM-H the effect of saturation diminishes. This supports an idea that enhanced thermal pressure of the magnetospheric plasma and ring current particles during magnetic storms results in the saturation of magnetic effect of the IMF Bz at the dayside magnetopause. A noticeable advantage of the model's prediction capabilities in comparison with other magnetopause models makes the model useful for space weather predictions.
Mechanisms underlying divergent relationships between Ca2+ and YAP/TAZ signaling

Yes-associated protein (YAP) and its homolog TAZ are transducers of several biochemical and biomechanical signals, serving to integrate multiplexed inputs from the microenvironment into higher-level cellular functions such as proliferation, differentiation, apoptosis, migration, and hemostasis. Emerging evidence suggests that Ca2+ is a key second messenger that closely connects microenvironmental input signals and YAP/TAZ regulation. However, studies that directly modulate Ca2+ have reported contradictory YAP/TAZ responses: In some studies, a reduction in Ca2+ influx increases the activity of YAP/TAZ, while in others, an increase in Ca2+ influx activates YAP/TAZ. Importantly, Ca2+ and YAP/TAZ exhibit distinct spatiotemporal dynamics, making it difficult to unravel their connections from a purely experimental approach. In this study, we developed a network model of Ca2+-mediated YAP/TAZ signaling to investigate how temporal dynamics and crosstalk of signaling pathways interacting with Ca2+ can alter YAP/TAZ response, as observed in experiments. By including six signaling modules (e.g., GPCR, IP3-Ca2+, Kinases, RhoA, F-actin, and Hippo-YAP/TAZ) that interact with Ca2+, we investigated both transient and steady-state cell response to Angiotensin II and thapsigargin stimuli. The model predicts stimuli, Ca2+ transient, and frequency-dependent relationships between Ca2+ and YAP/TAZ primarily mediated by signaling species like cPKC, DAG, CaMKII, and F-actin. Model results illustrate the role of Ca2+ dynamics and CaMKII bistable response in switching the direction of changes in Ca2+-induced YAP/TAZ activity for different stimuli. Frequency-dependent YAP/TAZ response revealed the competition between upstream regulators of LATS1/2, leading to the YAP/TAZ non-monotonic response to periodic GPCR stimulation. This study provides new insights into the underlying mechanisms responsible for the controversial Ca2+-YAP/TAZ relationship observed in experiments.
Low-cost and highly efficient: A method for high-quality nucleic acid isolation from cotton fibres

Gene expression analyses to study the development of cotton fibers require high-quality nucleic acid. The conventional methods of nucleic acid extraction results in sub-quality nucleic acids with low yields. Young fibers are rich in polyphenols and sugars that react with nucleic acid to form phenols and insoluble substances. Furthermore, mature fibers contain more than 95% cellulose, hindering the nucleic acid isolation. Cytoplasm collapse and cellulose deposition also result in a very low yield of nucleic acid. Three different methods of RNA isolation from different cotton tissues were compared in this study to determine the best and most efficient one. The integrity and quality of RNA were analyzed using UV spectrum, agarose gel electrophoresis, RIN values, PCR, and Northern blot hybridization. RNA of functional quality was observed when using the high ion and pH method, with an A260/A280 ratio up to 1.87 and an average yield of 0.68 mg g-1 from fiber cells. From leaves, we found an A260/A280 ratio of 2.02 and an average yield of 6.35 mg g-1, which is suitable for molecular biology experiments. The extraction buffer with a high ion density and pH value include Tris-HCl, LiCl, EDTA, SDS, sodium deoxycholate, Nonident P-40, mercaptoethanol, and PVP. The addition of sodium deoxycholate and Nonider-40 (NP-40) enhances the density of other salt compounds and elevates the pH value. The results depicted that the high ion and pH method is a simple and effective way to extract a copious amount of high-quality RNA from polysaccharide-rich tissues. This method is also suitable for the extraction of cotton genomic DNA with high purity. Genomic DNA extracted from cotton using this method showed an A260/A230 ratio up to 2.09 and a yield of 1.44 mg g-1. This method is useful for isolating DNA and RNA from cotton fibers and produces high yields and quality at a comparatively low cost.
The fate of recessive deleterious or overdominant mutations near mating-type loci under partial selfing

Large regions of suppressed recombination having extended over time occur in many organisms around genes involved in mating compatibility (sex-determining or mating-type genes). The sheltering of deleterious alleles has been proposed to be involved in such expansions. However, the dynamics of deleterious mutations partially linked to genes involved in mating compatibility are not well understood, especially in finite populations. In particular, under what conditions deleterious mutations are likely to be maintained for long enough near mating-compatibility genes remains to be evaluated, especially under selfing, which generally increases the purging rate of deleterious mutations. Using a branching process approximation, we studied the fate of a new deleterious or overdominant mutation in a diploid population, considering a locus carrying two permanently heterozygous mating-type alleles, and a partially linked locus at which the mutation appears. We obtained analytical and numerical results on the probability and purging time of the new mutation. We investigated the impact of recombination between the two loci and of the mating system (outcrossing, intra and inter-tetrad selfing) on the maintenance of the mutation. We found that the presence of a fungal-like mating-type locus (i.e. not preventing diploid selfing) always sheltered the mutation under selfing, i.e. it decreased the purging probability and increased the purging time of the mutations. The sheltering effect was higher in case of automixis (intra-tetrad selfing). This may contribute to explain why evolutionary strata of recombination suppression near the mating-type locus are found mostly in automictic (pseudo-homothallic) fungi. We also showed that rare events of deleterious mutation maintenance during strikingly long evolutionary times could occur, suggesting that deleterious mutations can indeed accumulate near the mating-type locus over evolutionary time scales. In conclusion, our results show that, although selfing purges deleterious mutations, these mutations can be maintained for very long times near a mating-type locus, which may contribute to promote the evolution of recombination suppression in sex-related chromosomes.
Seeing the future: Connectome strength and network efficiency in visual network predict individual ability of episodic future thinking

Episodic future thinking (EFT) refers to the critical ability that people construct vivid mental imagery about future events and pre-experience it, which helps with individual and group decision-making. Although EFT is generally believed to have a visual nature by theorists, little neuroscience evidence had been provided to verify this assumption. Here, by employing the approach of connectome-based predictive modeling (CPM) and graph-theoretical analysis, we analyzed resting-state functional brain image from 191 participants to predict their variability of EFT ability (leave-one-out cross-validation), and validated the results by applying different parcellation schemas and feature selection thresholds. At the connectome strength level, CPM-based analysis revealed that EFT ability could be predicted by the connectome strength of visual network. Further at the network level, graph-theoretical analysis showed that EFT ability could be predicted by the network efficiency of visual network. Moreover, these findings were replicated using different parcellation schemas and feature selection thresholds. These results robustly and collectively supported the visual network being the neural substrates underlying EFT ability from a comprehensive perspective of resting-state functional connectivity strength and the neural network. This study provides indications on how the function of visual network supports EFT ability, and helps to understand the EFT ability from a neural basis perspective.
The mesoglea buffers the physico-chemical microenvironment of photosymbionts in the upside-down jellyfish Cassiopea sp

The jellyfish Cassiopea has a conspicuous lifestyle, positioning itself upside-down on sediments in shallow waters thereby exposing its photosynthetic endosymbionts (Symbiodiniaceae) to light. Several studies have shown how the photosymbionts benefit the jellyfish host in terms of nutrition and O2 availability, but little is known about the internal physico-chemical microenvironment of Cassiopea during light-dark periods. Here, we used fiber-optic sensors to investigate how light is modulated at the water-tissue interface of Cassiopea sp. and how light is scattered inside host tissue. We additionally used electrochemical and fiber-optic microsensors to investigate the dynamics of O2 and pH in response to changes in the light availability in intact living specimens of Cassiopea sp. Mapping of photon scalar irradiance revealed a distinct spatial heterogeneity over different anatomical structures of the host, where oral arms and the manubrium had overall higher light availability, while shaded parts underneath the oral arms and the bell had less light available. White host pigmentation, especially in the bell tissue, showed higher light availability relative to similar bell tissue without white pigmentation. Microprofiles of scalar irradiance into white pigmented bell tissue showed intense light scattering and enhanced light penetration, while light was rapidly attenuated over the upper 0.5 mm in tissue with symbionts only. Depth profiles of O2 concentration into bell tissue of intact, healthy/living jellyfish showed increasing concentration with depth into the mesoglea, with no apparent saturation point during light periods. O2 was slowly depleted in the mesoglea in darkness, and O2 concentration remained higher than ambient water in large (> 6 cm diameter) individuals, even after 50 min in darkness. Light-dark shifts in large medusae showed that the mesoglea slowly turns from a net sink during photoperiods into a net source of O2 during darkness. In contrast, small medusae showed a more dramatic change in O2 concentration, with rapid O2 buildup/consumption in response to light-dark shifts; in a manner similar to corals. These effects on O2 production/consumption were also reflected in moderate pH fluctuations within the mesoglea. The mesoglea thus buffers O2 and pH dynamics during dark-periods.
The evolution of age-specific resistance to infectious disease

Innate, infection-preventing resistance often varies between host life-stages. Juveniles are more resistant than adults in some species, whereas the opposite pattern is true in others. This variation cannot always be explained by prior exposure or physiological constraints and so it has been hypothesised that trade-offs with other life-history traits may be involved. However, little is known about how trade-offs between various life-history traits and resistance at different life-stages affect the evolution of age-specific resistance. Here, we use a mathematical model to explore how trade-offs with natural mortality, reproduction and maturation combine to affect the evolution of resistance at different life-stages. Our results show that certain combinations of trade-offs have substantial effects on whether adults or juveniles are more resistant, with trade-offs between juvenile resistance and adult reproduction inherently more costly than trade-offs involving maturation or mortality (all else being equal), resulting in consistent evolution of lower resistance at the juvenile stage even when infection causes a lifelong fecundity reduction. Our model demonstrates how the differences between patterns of age-structured resistance seen in nature may be explained by variation in the trade-offs involved and our results suggest conditions under which trade-offs tend to select for lower resistance in juveniles than adults.
Simple scaling laws control the genetic architectures of human complex traits

Genome-wide association studies have revealed that the genetic architectures of complex traits vary widely, including in terms of the numbers, effect sizes, and allele frequencies of significant hits. However, at present we lack a principled way of understanding the similarities and differences among traits. Here, we describe a probabilistic model that combines mutation, drift, and stabilizing selection at individual sites with a genome-scale model of phenotypic variation. In this model, the architecture of a trait arises from the distribution of selection coefficients of mutations and from two scaling parameters. We fit this model for 95 diverse, highly polygenic quantitative traits from the UK Biobank. Notably, we infer similar distributions of selection coefficients across all these traits. This shared distribution implies that differences in architectures of highly polygenic traits arise mainly from the two scaling parameters: the mutational target size and heritability per site, which vary by orders of magnitude across traits. When these two scale factors are accounted for, the architectures of all 95 traits are nearly identical.
Non-Gaussian Normative Modelling With Hierarchical Bayesian Regression

Normative modelling is an emerging technique for parsing heterogeneity in clinical cohorts. This can be implemented in practice using hierarchical Bayesian regression, which provides an elegant probabilistic solution to handle site variation in a federated learning framework. However, applications of this method to date have employed a Gaussian assumption, which may be restrictive in some applications. We have extended the hierarchical Bayesian regression framework to flexibly model non-Gaussian data with heteroskdastic skewness and kurtosis. To this end, we employ a flexible distribution from the sinh-arcsinh (SHASH) family, and introduce a novel reparameterisation and a Markov chain Monte Carlo sampling approach to perform inference in this model. Using a large neuroimaging dataset collected at 82 different sites, we show that the results achieved with this extension are equivalent or better than a warped Bayesian linear regression baseline model on most datasets, whilst providing better control over the parameters governing the shape of distributions that approach is able to model. We also demonstrate that the attained flexibility is useful for accurately modelling highly nonlinear relationships between aging and imaging derived phenotypes, which shows that the extension is important for pushing the field of normative modelling forward. All methods described here are available in the open-source pcntoolkit. Highlights We extended the Hierarchical Bayesian Regression framework for normative modelling Our extension allows modelling data with heteroskedastic skewness and kurtosis We developed a reparameterization of the SHASH distribution, suitable for sampling We provide the first implementation of the SHASH distribution in a fully Bayesian framework Results show that the extension outperforms current methods on various measures
Transcriptome analysis during fruit developmental stages in durian (Durio zibethinus Murr.) var. D24

Durian (Durio zibethinus Murr.) fruits are famous for their unique aroma. This study analysed the Durian fruit transcriptome to discover the expression patterns of genes and to understand their regulation. Three developmental stages of Durian fruit, namely, early [90 days post-anthesis (DPA)], mature (120 DPA), and ripen (127 DPA), were studied. The Illumina HiSeq platform was used for sequencing. The sequence data were analysed using four different mapping aligners and statistical methods: CLC Genomic Workbench, HISAT2+DESeq2, Tophat+Cufflinks, and HISAT2+edgeR. The analyses showed that over 110 million clean reads were mapped to the Durian genome, yielding 19,976, 11,394, 17,833, and 24,351 differentially expressed genes during 90-127 days post-anthesis. Many identified differentially expressed genes were linked to the fruit ripening processes. The data analysis suggests that most genes with increased expression at the ripening stage were primarily involved in the metabolism of cofactors and vitamins, nucleotide metabolism, and carbohydrate metabolism. Significantly expressed genes from the young to mature stage were mainly associated with carbohydrate metabolism, amino acid metabolism, and cofactor and vitamin metabolism. The transcriptome data will serve as a foundation for understanding Durian fruit development-specific genes and could be helpful in fruit’s trait improvement.
An advanced sequence clustering and designation workflow reveals the enzootic maintenance of a dominant West Nile virus subclade in Germany

West Nile virus (WNV) is the most widespread arthropod-borne (arbo) virus and the primary cause of arboviral encephalitis globally. Members of WNV species genetically diverged and are classified into different hierarchical groups below species rank. However, the demarcation criteria for allocating WNV sequences into these groups remain individual, inconsistent, and the use of names for different levels of the hierarchical levels is unstructured. In order to have an objective and comprehensible grouping of WNV sequences, we developed an advanced grouping workflow using the “affinity propagation clustering”-algorithm and newly included the “agglomerative hierarchical clustering”-algorithm for the allocation of WNV sequences into different groups below species rank. In addition, we propose to use a fixed set of terms for the hierarchical naming of WNV below species level and a clear decimal numbering system to label the determined groups. For validation, we applied the refined workflow to WNV sequences that have been previously grouped into various lineages, clades, and clusters in other studies. Although our workflow regrouped some WNV sequences, overall, it generally corresponds with previous groupings. We employed our novel approach to the sequences from the WNV circulation in Germany 2020, primarily from WNV-infected birds and horses. Besides two newly defined minor (sub)clusters comprising only of three sequences each, subcluster 2.5. 3.4. 3c was the predominant WNV sequence group detected in Germany from 2018-20. This predominant subcluster was also associated with at least five human WNV-infections in 2019-20. In summary, our analyses imply that the genetic diversity of the WNV population in Germany is shaped by enzootic maintenance of the dominant WNV subcluster accompanied by sporadic incursions of other rare clusters and subclusters. Moreover, we show that our refined approach for sequence grouping yields meaningful results. Although we primarily aimed at a more detailed WNV classification, the presented workflow can also be applied to the objective genotyping of other virus species.
Chromosome assembly for the meagre, Argyrosomus regius, reveals species adaptations and sciaenid sex-related locus evolution

The meagre, Argyrosomus regius, has recently become a species of increasing economic interest for the Mediterranean aquaculture and there is ongoing work to boost production efficiency through selective breeding. Access to the complete genomic sequence will provide an essential resource for studying quantitative trait-associated loci and exploring the genetic diversity of different wild populations and aquaculture stocks in more detail. Here, we present the first complete genome for A. regius, produced through a combination of long and short read technologies and an efficient in-house developed pipeline for assembly and polishing. Scaffolding using previous linkage map data allowed us to reconstruct a chromosome level assembly with high completeness, complemented with gene annotation and repeat masking. We use this new resource to study the evolution of the meagre genome and other Sciaenids, via a comparative analysis of 25 high-quality teleost genomes. Combining a rigorous investigation of gene duplications with base-wise conservation analysis, we identify candidate loci related to immune, fat metabolism and growth adaptations in the meagre. Following phylogenomic reconstruction, we show highly conserved synteny within Sciaenidae. In contrast, we report rapidly evolving syntenic rearrangements and gene copy changes in the sex-related dmrt1 neighbourhood in meagre and other members of the family. These novel genomic datasets and findings will add important new tools for aquaculture studies and greatly facilitate husbandry and breeding work in the species.