Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatial and Temporal Analysis of SARS-CoV-2 Genome Evolutionary Patterns

The spread of SARS-CoV-2 virus accompanied by availability of abundant sequence data publicly, provides a window for determining the spatio-temporal patterns of viral evolution in response to vaccination. In this study, SARS-CoV-2 genome sequences were collected from seven countries in the period January 2020-December 2022. The sequences were classified into three phases, namely: pre-vaccination, post-vaccination, and recent period. Comparison was performed between these phases based on parameters like mutation rates, selection pressure (dN/dS ratio), and transition to transversion ratios (Ti/Tv). Similar comparisons were performed among SARS-CoV-2 variants. Statistical significance was tested using Graphpad unpaired t-test. The comparative analysis showed an increase in the percent genomic mutation rates post-vaccination and in recent periods across different countries from the pre-vaccination phase. The dN/dS ratios showed positive selection that increased after vaccination, and the Ti/Tv ratios decreased after vaccination. C→U and G→U were the most frequent transitions and transversions in all the countries. However, U→G was the most frequent transversion in recent period. The Omicron variant had the highest genomic mutation rates, while Delta showed the highest dN/dS ratio. Mutation rates were highest in NSP3, S, N and NSP12b before and increased further after vaccination. NSP4 showed the largest change in mutation rates after vaccination. N, ORF8, ORF3a and ORF10 were under highest positive selection before vaccination. They were overtaken by E, S and NSP1 in the after vaccination as well as recent sequences, with the largest change observed in NSP1. Protein-wise dN/dS ratio was also seen to vary across the different variants. Importance Irrespective of the different vaccine technologies used, geographical regions and host genetics, variations in the SARS-CoV-2 genome have maintained similar patterns worldwide. To the best of our knowledge, there exists no other large-scale study of the genomic and protein-wise mutation patterns during the time course of evolution in different countries. Analysing the SARS-CoV-2 evolution patterns in response to spatial, temporal, and biological signals is important for diagnostics, therapeutics, and pharmacovigilance of SARS-CoV-2.
Jointly efficient encoding and decoding in neural populations

The efficient coding approach proposes that neural systems represent as much sensory information as biological constraints allow. It aims at formalizing encoding as a constrained optimal process. A different approach, that aims at formalizing decoding, proposes that neural systems instantiate a generative model of the sensory world. Here, we put forth a normative framework that characterizes neural systems as jointly optimizing encoding and decoding. It takes the form of a variational autoencoder: sensory stimuli are encoded in the noisy activity of neurons to be interpreted by a flexible decoder; encoding must allow for an accurate stimulus reconstruction from neural activity. Jointly, neural activity is required to represent the statistics of latent features which are mapped by the decoder into distributions over sensory stimuli; decoding correspondingly optimizes the accuracy of the generative model. This framework results in a family of encoding-decoding models, which result in equally accurate generative models, indexed by a measure of the stimulus-induced deviation of neural activity from the prior distribution over neural activity. Each member of this family predicts a specific relation between properties of the sensory neurons—such as the arrangement of the tuning curve means (preferred stimuli) and widths (degrees of selectivity) in the population—as a function of the statistics of the sensory world. Our approach thus generalizes the efficient coding approach. Notably, here, the form of the constraint on the optimization derives from the requirement of an accurate generative model, while it is arbitrary in efficient coding models. Finally, we characterize the family of models we obtain through other measures of performance, such as the error in stimulus reconstruction. We find that a range of models admit comparable performance; in particular, a population of sensory neurons with broad tuning curves as observed experimentally yields both low reconstruction stimulus error and an accurate generative model.
Differing structures of galactoglucomannan in eudicots and non-eudicot angiosperms

The structures of cell wall mannan hemicelluloses have changed during plant evolution. Recently, a new structure called β-galactoglucomannan (β-GGM) was discovered in eudicot plants. This galactoglucomannan has β-(1,2)-Gal-α-(1,6)-Gal disaccharide branches on some mannosyl residues of the strictly alternating Glc-Man backbone. Studies in Arabidopsis revealed β-GGM is related in structure, biosynthesis and function to xyloglucan. However, when and how plants acquired β-GGM remains elusive. Here, we studied mannan structures in many sister groups of eudicots. All glucomannan structures were distinct from β-GGM. In addition, we searched for candidate mannan β-galactosyltransferases (MBGT) in non-eudicot angiosperms. Candidate AtMBGT1 orthologues from rice and Amborella did not show MBGT activity in vivo. However, the AtMBGT1 orthologue from rice showed MUR3-like xyloglucan galactosyltransferase activity in complementation analysis using Arabidopsis. Further, reverse genetic analysis revealed that the enzyme contributes to proper root growth in rice. Together, gene duplication and diversification of GT47A-VII in eudicot evolution may have been involved in the acquisition of mannan β-galactosyltransferase activity. Our results indicate that β-GGM is likely to be a eudicot-specific mannan.
Does the seed fall far from the tree? Weak fine-scale genetic structure in a continuous Scots pine population

Knowledge of fine-scale spatial genetic structure, i.e., the distribution of genetic diversity at short distances, is important in evolutionary research and in practical applications such as conservation and breeding programs. In trees, related individuals often grow close to each other due to limited seed and/or pollen dispersal. The extent of seed dispersal also limits the speed at which a tree species can spread to new areas. We studied the fine-scale spatial genetic structure of Scots pine (Pinus sylvestris) in two naturally regenerated sites located 20 km from each other in continuous south-eastern Finnish forest. We genotyped almost 500 adult trees for 150k SNPs using a custom made Affymetrix array. We detected some pairwise relatedness at short distances, but the average relatedness was low and decreased with increasing distance, as expected. Despite the clustering of related individuals, the sampling sites were not differentiated (FST = 0.0005). According to our results, Scots pine has a large neighborhood size (Nb = 1680– 3210), but a relatively short gene dispersal distance (σg = 36.5–71.3 m). Knowledge of Scots pine fine-scale spatial genetic structure can be used to define suitable sampling distances for evolutionary studies and practical applications. Detailed empirical estimates of dispersal are necessary both in studying post-glacial recolonization and predicting the response of forest trees to climate change.
PDF neuropeptide signals independently of Bruchpilot-labelled active zones in daily remodelled terminals of Drosophila clock neurons

The small ventrolateral neurons (sLNvs) are key components of the central clock in the Drosophila brain. They signal via the neuropeptide Pigment-dispersing factor (PDF) to align the molecular clockwork of different central clock neurons and to modulate downstream circuits. The dorsal terminals of the sLNvs undergo daily morphological changes that have been shown to affect presynaptic sites organised by the active zone protein Bruchpilot (BRP), a homolog of mammalian ELKS proteins. Although the circadian plasticity of the sLNv terminals is well established, whether and how it is related to the rhythmic release of PDF remains ill-defined. Here, we combined expansion microscopy with labelling of active zones by endogenously tagged BRP to examine the spatial correlation between PDF-containing dense-core vesicles and BRP-labelled active zones. We found that the number of BRP-labelled punctae in the sLNv terminals remained stable while their density changed during circadian plasticity. The relative distance between BRP- and PDF-labelled punctae was increased in the morning, around the reported time of PDF release. Spontaneous dense-core vesicle release profiles of the sLNvs in a publicly available ssTEM dataset (FAFB) consistently lacked spatial correlation to BRP-organised active zones. RNAi-mediated downregulation of brp and other active zone proteins expressed by the sLNvs did not affect PDF-dependent locomotor rhythmicity. In contrast, down-regulation of genes of the canonical vesicle release machinery, the dense-core vesicle-related protein CADPS, as well as PDF impaired locomotor rhythmicity. Taken together, our study suggests that PDF release from the sLNvs is independent of BRP-organised active zones which seem not to be circadianly destroyed and re-established.
Resistance towards and biotransformation of Pseudomonas-produced secondary metabolites during community invasion

The role of antagonistic secondary metabolites produced by Pseudomonas protegens in suppression of soil-borne phytopathogens has been clearly documented. However, their contribution to the ability of P. protegens to establish in soil and rhizosphere microbiomes remains ambiguous. Here, we use a four-species synthetic community to determine how antibiotic production contributes to P. protegens community invasion and identify community traits that alter the abundance of key P. protegens antimicrobial metabolites (DAPG, pyoluteorin and orfamide A). Surprisingly, mutants deficient in antimicrobial production caused similar perturbations in community composition compared to invasion by wildtype P. protegens. Intriguingly, while pyoluteorin and orfamide A are secreted at levels toxic to individual bacterial strains, community-level resistance circumvents toxicity. Here, we identify the underlying mechanism by which the cyclic lipopeptide, orfamide A, is inactivated and degraded by Rhodococcus globerulus D757 and Stenotrophomonas indicatrix D763. Altogether, the demonstration that the synthetic community constrains P. protegens invasion by detoxifying its antibiotics may provide a mechanistic explanation to inconsistencies in biocontrol effectiveness in situ.
Pan-genome analysis of six complete Paracoccus type strain genomes from hybrid next generation sequencing

The genus Paracoccus capable of inhabiting a variety of different ecological niches both, marine and terrestrial is globally distributed. In addition, Paracoccus is taxonomically, metabolically and regarding lifestyle highly diverse. Until now, little is known on how Paracoccus can adapt to such a range of different ecological niches and lifestyles. In the present study, the genus Paracoccus was phylogenomically analyzed (n = 160) and revisited, allowing species level classification of 16 so far unclassified Paracoccus sp. strains and detection of five misclassifications. Moreover, we performed pan-genome analysis of Paracoccus-type strains, isolated from a variety of ecological niches, including different soils, tidal flat sediment, host association such as the bluespotted cornetfish, Bugula plumosa, and the reef-building coral Stylophora pistillata to elucidate either i) the importance of lifestyle and adaptation potential, and ii) the role of the genomic equipment and niche adaptation potential. Six complete genomes were de novo hybrid assembled using a combination of short and long-read technologies. These Paracoccus genomes increase the number of completely closed high-quality genomes of type strains from 15 to 21. Pan-genome analysis revealed an open pan-genome composed of 13,819 genes with a minimal chromosomal core (8.84 %) highlighting the genomic adaptation potential and the huge impact of extra-chromosomal elements. All genomes are shaped by the acquisition of various mobile genetic elements including genomic islands, prophages, transposases, and insertion sequences emphasizing their genomic plasticity. In terms of lifestyle, each mobile genetic elements should be evaluated separately with respect to the ecological context. Free- living genomes, in contrast to host-associated, tend to comprise (1) larger genomes, or the highest number of extra-chromosomal elements, (2) higher number of genomic islands and insertion sequence elements, and (3) a lower number of intact prophage regions. Due to the vast number of adaptive genes, Paracoccus can quickly adapt to changing environmental conditions.
Bifurcation of solutions through a contact manifold in bidisperse models

This research focuses on a hyperbolic system that describes bidisperse suspensions, consisting of two types of small particles dispersed in a viscous fluid. The dependence of solutions on the relative position of contact manifolds in the phase space is examined. The wave curve method serves as the basis for the first and second analyses. The former involves the classification of elementary waves that emerge from the origin of the phase space. Analytical solutions to prototypical Riemann problems connecting the origin with any point in the state space are provided. The latter focuses on semi-analytical solutions for Riemann problems connecting any state in the phase space with the maximum packing concentration line, as observed in standard batch sedimentation tests. When the initial condition crosses the first contact manifold, a bifurcation occurs. As the initial condition approaches the second manifold, another structure appears to undergo bifurcation, although it does not represent an actual bifurcation according to the triple shock rule. The study reveals important insights into the behavior of solutions in relation to these contact manifolds. This research sheds light on the existence of emerging quasi-umbilic points within the system, which can potentially lead to new types of bifurcations as crucial elements of the elliptic/hyperbolic boundary in the system of partial differential equations. The implications of these findings and their significance are discussed.
Three-dimensional computed tomography mapping techniques in the morphometric analysis of AO/OTA 33A and 33C distal femoral fractures: a retrospective single-center study

Purpose: Complex distal femoral fractures involve a challenging set of considerations that must be known to provide optimal management. This study aimed to determine the location and frequency of fracture lines and comminution zones in AO/OTA types 33A and 33C distal femoral fractures using three-dimensional computed tomography mapping. Methods: Seventy-four consecutive eligible patients were included. Fracture fragments for each patient were reconstructed, virtually reduced, and adjusted to match the distal femoral template. Then, all fracture lines and comminuted areas were extracted in transparent mode, and corresponding heat maps were constructed. Finally, these maps, along with the quantitative analysis findings of the counts and volumes of each fragment, were used to summarize the characteristics of the fractures. Results: Thirty-four females and 40 males [average age, 58 years (range, 18–92 years)] presented with a distal femoral fracture. There were 53 AO/OTA type 33A fractures, and 21 AO/OTA type 33C fractures. These two patterns differed significantly on fracture fragment count, comminuted zone fracture fragment count, and mean comminuted zone fracture fragment volume (p < 0.05). Most of the fracture line heat zones were in the femoral epiphysis, intercondylar notch of the femur, and patellofemoral joint. The comminuted area heat regions were mostly found on the lateral, anterior, and posterior femoral diaphysis, with less involvement on the medial side. Conclusion: Our findings may serve as a guide for the surgical approach selection of complex distal femur fractures, the placement strategy of the internal fixation, and the optimization of the osteotomy plan for biomechanical studies.
Dynamic changes of soil microorganisms in rotation farmland at the western foot of the Greater Khingan range

Crop rotation and other tillage systems can affect soil microbial communities and functions. Few studies have reported the response of soil spatial microbial communities to rotation under drought stress. Therefore, the purpose of our study was to explore the dynamic changes of the soil space microbial community under different drought stress-rotation patterns. In this study, two water treatments were set up, control W1 (mass water content 25%–28%), and drought W2 (mass water content 9%–12%). Four crop rotation patterns were set in each water content, spring wheat continuous (R1), spring wheat-potato (R2), spring wheat-potato-rape (R3) and spring wheat-rape (R4), for a total of eight treatments (W1R1, W1R2, W1R3, W1R4, W2R1, W2R2, W2R3, W2R4). Endosphere, rhizosphere and bulk soil of spring wheat in each treatment were collected, and root space microbial community data were generated. The soil microbial community changed under different treatments and their relationship with soil factors were analyzed using a co-occurrence network, mantel test, and other methods. The results revealed that the alpha diversity of microorganisms in the rhizosphere and bulk soil did not differ significantly, but it was significantly greater than in the endosphere. The bacteria community structure was more stable, fungi alpha-diversity significant changes (p < 0.05), that were more sensitive to the response of various treatments than bacteria. The co-occurrence network between fungal species was stable under rotation patterns (R2, R3, R4), while the community stability was poor under continuous cropping pattern (R1), and interactions were strengthened. Soil organic matter (SOM), microbial biomass carbon (MBC), and pH value were the most important factors dominating the bacteria community structural changed in the endosphere, rhizosphere, and bulk soil. The dominant factor that affected the fungal community structural changed in the endosphere, rhizosphere, and bulk soil was SOM. Therefore, we conclude that soil microbial community changes under the drought stress-rotation patterns are mainly influenced by soil SOM and microbial biomass content.
Automated Classification for Celestial Spectra Based on Cover Algorithm

Automated classification for large numbers of celestial spectra is one of the most important problems which are urgent to be solved in large survey projects.In this paper,an automated classification method for celestial spectra based on cover algorithm is presented.In the training procedure,some representative spectra of the training spectrum set can be obtained by utilizing a certain cover rule.Then,in the classification phase,the classifier computes the distances between each test spectrum and the representatives,and the class of the test spectrum is determined by the representative spectrum closest to the test spectrum.The experimental results show that this method is better than SVM both in training speed and classifying accuracy over Normal Galaxies (NGs),Stars,Active Galaxies(AGs)and Active Galactic Nucleus(AGNs)datasets.And the proposed method is promising for the automated classification of large numbers of celestial spectra collected by large survey projects.
Water pH, not soil pH, alters bacterial community structural pattern and nitrogen cycling pathways in date palm (Phoenix dactylifera L.) roots and bulk soil under freshwater irrigation regime

Date palms are widely cultivated in arid agroecosystems, where knowledge of irrigation water effect on their soil and root-associated bacterial communities is limited. Using 16S rDNA metabarcoding, we studied soil and root-associated bacterial communities of date palms growing in United Arab Emirates. Overall, 12.18% of bacterial operational taxonomic units (OTUs) were unique to roots, whereas 41.55% were specific to soil. The bacterial diversity was lower in root and community patterns were distinct between compartments, wherein irrigation water pH was a key structuring factor in both compartments, while salinity (electrical conductivity) was important only in the soil. Co-occurrence network analysis revealed a decrease in complexity in the soil–root continuum, and specific taxa/modules also varied with water pH. We observed a higher abundance of endophyte–saprotroph (Bacillus, Streptomyces and Dongia) dual-role OTUs in both compartments, possibly involved in nutrient mobilisation and plant growth. Based on PICRUSt and trait-based analyses, we showed that these OTUs are putatively involved in the nitrogen cycle (nitrification, denitrification, and assimilatory nitrate reduction). Taken together, we suggest that irrigation water pH, not soil pH, transiently affects belowground bacterial communities and selects bacteria in specific pH ranges, which may be important for nutrient cycling (i.e. nitrogen cycle) in arid agroecosystems.
How molecular advances may improve the diagnosis and management of PTCL patients

Peripheral T-cell lymphomas (PTCL) comprised more than 30 rare heterogeneous entities, representing 10 to 15% of adult non-Hodgkin lymphomas. Although their diagnosis is still mainly based on clinical, pathological, and phenotypic features, molecular studies have allowed for a better understanding of the oncogenic mechanisms involved and the refinement of many PTCL entities in the recently updated classifications. The prognosis remains poor for most entities (5-year overall survival < 30%), with current conventional therapies based on anthracyclin-based polychemotherapy regimen, despite many years of clinical trials. The recent use of new targeted therapies appears to be promising for relapsed/refractory patients, such as demethylating agents in T-follicular helper (TFH) PTCL. However further studies are needed to evaluate the proper combination of these drugs in the setting of front-line therapy. In this review, we will summarize the oncogenic events for the main PTCL entities and report the molecular targets that have led to the development of new therapies. We will also discuss the development of innovative high throughput technologies that aid the routine workflow for the histopathological diagnosis and management of PTCL patients.
Advances in dynamic visual acuity test research

The dynamic visual acuity test (DVAT) is a functional evaluation tool for the impairment and compensation of the vestibular system, which could reflect the Vestibulo-ocular reflex (VOR) function. We present an overview of DVAT research, displaying recent advances in test methods, application, and influencing factors; and discussing the clinical value of DVAT to provide a reference for clinical application. There are two primary types of DVAT: dynamic-object DVAT and static-object DVAT. For the latter, in addition to the traditional bedside DVAT, there are numerous other approaches, including Computerized DVAT (cDVAT), DVAT on a treadmill, DVAT on a rotary, head thrust DVA (htDVA) and functional head impulse testing (fHIT), gaze shift dynamic visual acuity with walking (gsDVA), translational dynamic visual acuity test (tDVAT), pediatric DVAT. The results of DAVT are affected by subject [occupation, static visual acuity (SVA), age, eyeglass lenses], testing methods, caffeine, and alcohol. DVAT has numerous clinical applications, such as screening for vestibular impairment, assessing vestibular rehabilitation, predicting fall risk, and evaluating ophthalmology-related disorders, vestibular disorders, and central system disorders.