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Collagen crosslinking employing ultraviolet A rays and riboflavin (UVA/R) has emerged as a pivotal technique in clinical therapies, especially in ophthalmology since the 1990s. Despite its clinical adoption, the lack of clarity of the detailed mechanism and the imperative for a refined manufacturing process necessitates further investigation. This study advances the understanding of UVA/R crosslinked collagen, concentrating on identifying the primary crosslinking sites using seven synthetic peptides and exploring the pathways of riboflavin‐mediated crosslinking. The results demonstrate that tyrosine residues are key crosslinking sites, and riboflavin plays a dual role as both a catalyst and a competitive inhibitor in the crosslinking process. Furthermore, the UVA/R crosslinked collagen matrix exhibits a more harmonious balance between stability and degradability compared with chemically crosslinked collagen matrices, coupled with superior mechanical properties and augmented biocompatibility. In vivo experiments further validate its excellent biocompatibility, reduced tissue inflammation, and promotion of tissue regeneration. The research provides crucial insights into collagen crosslinking mechanisms, paving the way for the development of sophisticated collagen‐based biomaterials tailored for biomedical applications. [ABSTRACT FROM AUTHOR]

Motivation Long-read RNA sequencing enables the mapping of RNA modifications, structures, and protein-interaction sites at the resolution of individual transcript isoforms. To understand the functions of these RNA features, it is critical to analyze them in the context of transcriptomic and genomic annotations, such as open reading frames and splice junctions. Results We have developed R2Dtool, a bioinformatics tool that integrates transcript-mapped information with transcript and genome annotations, allowing for the isoform-resolved analytics and graphical representation of RNA features in their genomic context. We illustrate R2Dtool's capability to integrate and expedite RNA feature analysis using epitranscriptomics data. R2Dtool facilitates the comprehensive analysis and interpretation of alternative transcript isoforms. Availability and implementation R2Dtool is freely available under the MIT license at github.com/comprna/R2Dtool. [ABSTRACT FROM AUTHOR]

Circular RNAs (circRNAs) exhibit unique properties due to their covalently closed nature. Models of circRNAs synthesis and function are emerging but much remains undefined about this surprisingly prevalent class of RNA. Here, we identified exonic circRNAs from human and mouse RNA-sequencing datasets, documenting multiple new examples. Addressing function, we found that many circRNAs co-sediment with ribosomes, indicative of their translation potential. By contrast, circRNAs with potential to act as microRNA sponges were scarce, with some support for a collective sponge function by groups of circRNAs. Addressing circRNA biogenesis, we delineated several features commonly associated with circRNA occurrence. CircRNA-producing genes tend to be longer and to contain more exons than average. Back-splice acceptor exons are strongly enriched at ordinal position 2 within genes, and circRNAs typically have a short exon span with two exons being the most prevalent. The flanking introns either side of circRNA loci are exceptionally long. Of note also, single-exon circRNAs derive from unusually long exons while multi-exon circRNAs are mostly generated from exons of regular length. These findings independently validate and extend similar observations made in a number of prior studies. Furthermore, we analysed high-resolution RNA polymerase II occupancy data from two separate human cell lines to reveal distinctive transcription dynamics at circRNA-producing genes. Specifically, RNA polymerase II traverses the introns of these genes at above average speed concomitant with an accentuated slow-down at exons. Collectively, these features indicate how a perturbed balance between transcription and linear splicing creates important preconditions for circRNA production. We speculate that these preconditions need to be in place so that looping interactions between flanking introns can promote back-splicing to raise circRNA production to appreciable levels. [ABSTRACT FROM AUTHOR]

SUMMARY: Transcript stability is an important determinant of its abundance and, consequently, translational output. Transcript destabilisation can be rapid and is well suited for modulating the cellular response. However, it is unclear the extent to which RNA stability is altered under changing environmental conditions in plants. We previously hypothesised that recovery‐induced transcript destabilisation facilitated a phenomenon of rapid recovery gene downregulation (RRGD) in Arabidopsis thaliana (Arabidopsis) following light stress, based on mathematical calculations to account for ongoing transcription. Here, we test this hypothesis and investigate processes regulating transcript abundance and fate by quantifying changes in transcription, stability and translation before, during and after light stress. We adapt syringe infiltration to apply a transcriptional inhibitor to soil‐grown plants in combination with stress treatments. Compared with measurements in juvenile plants and cell culture, we find reduced stability across a range of transcripts encoding proteins involved in RNA binding and processing. We also observe light‐induced destabilisation of transcripts, followed by their stabilisation during recovery. We propose that this destabilisation facilitates RRGD, possibly in combination with transcriptional shut‐off that was confirmed for HSP101, ROF1 and GOLS1. We also show that translation remains highly dynamic over the course of light stress and recovery, with a bias towards transcript‐specific increases in ribosome association, independent of changes in total transcript abundance, after 30 min of light stress. Taken together, we provide evidence for the combinatorial regulation of transcription and stability that occurs to coordinate translation during light stress and recovery in Arabidopsis. Significance Statement: We provide a method for administering the transcriptional inhibitor, cordycepin, to mature Arabidopsis leaves. We study changes in mRNA stability and translation during light stress and recovery. [ABSTRACT FROM AUTHOR]

Aims: Oak–hornbeam forests and related vegetation types (phytosociological order Carpinetalia betuli) are widespread in temperate western Eurasia. However, their national classification systems are poorly compatible, and a broad‐scale classification based on numerical analyses is lacking. Therefore, we aimed to establish a unified formalized classification system based on a large data set of vegetation plots covering the entire range of these forests. Location: Europe, Anatolia, Caucasus and northern Iran. Methods: We compiled a data set of 15,817 vegetation plots from the European Vegetation Archive and the Hyrcanian Forest Vegetation Database, using the formal definition of the EUNIS habitat type T1E Carpinus and Quercus mesic deciduous forest. We classified the data set using TWINSPAN. Biogeographically and ecologically similar plot clusters were merged into oak–hornbeam forest types, which were interpreted as alliances. We also developed expert systems for automatically classifying vegetation at the alliance level for both the EuroVegChecklist (EVC) system and the revised classification. In addition, we calculated ordinations to show the major gradients in the species composition of the data set. Results: We present a revised classification system of the order Carpinetalia betuli with nine alliances, including basic descriptions of their species composition, distribution, ecology and syntaxonomy. The analyses largely supported the biogeographic concept of classification, analogous to EVC. Compared to EVC, we recognized an additional alliance Physospermo verticillati‐Quercion cerridis (southern Italy) but found no support for the alliances Astrantio‐Carpinion, Erythronio‐Carpinion and Scillo‐Quercion. The greatest difference in species composition was found between the southern and northern‐northeastern Carpinetalia types. Expert systems for the revised classification system (~89% of plots classified) and the EVC system (~72%) are also included. Conclusions: We provide the first comprehensive overview of alliances of the order Carpinetalia betuli across its whole distribution range. The associated expert systems allow consistent application of the classification of these forests in nature conservation, habitat monitoring, and biodiversity and ecological research.We provide the first formal classification for oak–hornbeam forests and related vegetation types (phytosociological order Carpinetalia betuli) across Europe and adjacent areas. It includes both traditional and revised classifications of this vegetation. Furthermore, we developed expert systems for vegetation‐plot assignment to vegetation types, which can be applied in research and biodiversity conservation, monitoring and management. [ABSTRACT FROM AUTHOR]

Abstract—The climatic characteristics and morphometric indicators of the relief of habitats of forest communities described in the system of ecological and floristic classification on the Ufa plateau, as well as on the western macroslope and in the centrally elevated part of the Southern Urals were compared. It has been shown that syntaxonomic differences in forest vegetation in these areas are primarily caused by the differences in air temperature and summer precipitation. Existing climate change forecasts assume an increase in average annual and summer temperatures, as well as an increase in the amount of winter and a decrease in summer precipitation. This suggests that coniferous and mixed coniferous-broad-leaved forests will be enriched with species of the nemoral complex in the future in the Southern Urals, which in turn will lead to an increase in their similarity with modern forests of the Ufa plateau. [ABSTRACT FROM AUTHOR]

The article presents the results of complex research (research was conducted in 2019) of the Botanical natural monument territory "Pine forest near Venetsiya village" (Russia). In 2007, part of the nature monument territory was destroyed by a hurricane, resulting in massive windfall. The purpose of the research was to study the processes of evolution of natural complexes (vegetation and soil cover) in the areas affected by the hurricane. Classification of vegetation was done according to the Braun-Blanquet and Kopečký and Hejný approaches. NDVI (Normalized Difference Vegetation Index) was used to estimate the amount of photosynthetically active biomass. Changes in morphological, physical and chemical properties were studied in the soil cover. The conducted research showed that the vegetation of the natural monument is represented by relict pine and broad-leaved pine forests. Under the pine canopy linden and birch are dominated. In the herb layer grow in various combinations of nemoral and boreal species. Soil cover is represented by Gray-humus (Umbric Luvisol). There is a strong transformation of vegetation in the areas damaged by the hurricane in 12 years (2007-2019). There is an active formation of highly productive herbaceous vegetation and renewal of deciduous stands, which leads to an increase in biomass (confirmed by changes in NDVI). The terminal stage of the restoration succession will be the formation of secondary deciduous and mixed nemoral forests. The active development of grass vegetation leads to the formation of a sod horizon on the surface of the soil with a thickness of about 14 cm. There is also an increase in the content of organic carbon, alkaline-hydrolyzable nitrogen and mobile phosphorus, the value of electrical resistivity increases and acidification of the soil solution. [ABSTRACT FROM AUTHOR]

We consider the problem of inductive matrix completion, i.e., the reconstruction of a matrix using side features of its rows and columns. In numerous applications, however, side information of this kind includes redundant or uninformative features, so feature selection is required. An approach based on matrix factorization with group LASSO regularization on the coefficients of the side features is proposed, which combines feature selection with matrix completion. It is proved that the theoretical sample complexity for the proposed approach is lower than for methods without sparsifying. A computationally efficient iterative procedure for simultaneous matrix completion and feature selection is proposed. Experiments on synthetic and real-world data demonstrate that, due to the feature selection procedure, the proposed approach outperforms other methods. [ABSTRACT FROM AUTHOR]

• Usage of most spatially detailed feature maps boosts classification quality within the proposed multitask framework. • A deep convolutional network for triage of COVID-19 patients based on identification and severity quantification scores. • A carefully selected independent external test set with other lung pathologies. • Publicly released annotated data and code to ensure reproducibility. [Display omitted] The current COVID-19 pandemic overloads healthcare systems, including radiology departments. Though several deep learning approaches were developed to assist in CT analysis, nobody considered study triage directly as a computer science problem. We describe two basic setups: Identification of COVID-19 to prioritize studies of potentially infected patients to isolate them as early as possible; Severity quantification to highlight patients with severe COVID-19, thus direct them to a hospital or provide emergency medical care. We formalize these tasks as binary classification and estimation of affected lung percentage. Though similar problems were well-studied separately, we show that existing methods could provide reasonable quality only for one of these setups. We employ a multitask approach to consolidate both triage approaches and propose a convolutional neural network to leverage all available labels within a single model. In contrast with the related multitask approaches, we show the benefit from applying the classification layers to the most spatially detailed feature map at the upper part of U-Net instead of the less detailed latent representation at the bottom. We train our model on approximately 1500 publicly available CT studies and test it on the holdout dataset that consists of 123 chest CT studies of patients drawn from the same healthcare system, specifically 32 COVID-19 and 30 bacterial pneumonia cases, 30 cases with cancerous nodules, and 31 healthy controls. The proposed multitask model outperforms the other approaches and achieves ROC AUC scores of 0.87 ± 0.01 vs. bacterial pneumonia, 0.93 ± 0.01 vs. cancerous nodules, and 0.97 ± 0.01 vs. healthy controls in Identification of COVID-19, and achieves 0.97 ± 0.01 Spearman Correlation in Severity quantification. We have released our code and shared the annotated lesions masks for 32 CT images of patients with COVID-19 from the test dataset. [ABSTRACT FROM AUTHOR]

Translational control targeting the initiation phase is central to the regulation of gene expression. Understanding all of its aspects requires substantial technological advancements. Here we modified yeast translation complex profile sequencing (TCP-seq), related to ribosome profiling, and adapted it for mammalian cells. Human TCP-seq, capable of capturing footprints of 40S subunits (40Ss) in addition to 80S ribosomes (80Ss), revealed that mammalian and yeast 40Ss distribute similarly across 5′TRs, indicating considerable evolutionary conservation. We further developed yeast and human selective TCP-seq (Sel-TCP-seq), enabling selection of 40Ss and 80Ss associated with immuno-targeted factors. Sel-TCP-seq demonstrated that eIF2 and eIF3 travel along 5′ UTRs with scanning 40Ss to successively dissociate upon AUG recognition; notably, a proportion of eIF3 lingers on during the initial elongation cycles. Highlighting Sel-TCP-seq versatility, we also identified four initiating 48S conformational intermediates, provided novel insights into ATF4 and GCN4 mRNA translational control, and demonstrated co-translational assembly of initiation factor complexes. • Selective TCP-seq dissects translation mechanisms in mammals and yeast • 40S-bound eIF2 and eIF3 traverse 5′ UTRs and sequentially dissociate at AUG codons • AUG recognition involves four conformational intermediates of the 48S PIC • Initiation factors can assemble co-translationally into higher-order complexes Changing environmental conditions require reprogramming of gene expression for cells to adapt and survive. Translational control is central to this complex response. Wagner et al. developed assays capturing footprints of mRNA-bound ribosomal complexes associated with selected translation-promoting factors to uncover mechanisms underlying translation in the context of its regulatory potential. [ABSTRACT FROM AUTHOR]