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Lariat formation has been studied intensively only with a few self‐splicing group II introns, and little is known about how the numerous diverse introns in plant organelles are excised. Several of these introns have branch‐points that are not a single bulge but are adjoined by A:A, A:C, A:G and G:G pairs. Using a highly sensitive in vivo approach, we demonstrate that all but one of the barley chloroplast introns splice via the common pathway that produces a branched product. RNA editing does not improve domain 5 and 6 structures of these introns. The conserved branch‐point in tobacco rpl16 is chosen even if an adjacent unpaired adenosine is available, suggesting that spatial arrangements in domain 6 determine correct branch‐point selection. Lariats were not detected for the chloroplast trnV intron, which lacks an unpaired adenosine in domain 6. Instead, this intron is released as linear molecules that undergo further polyadenylation. trnV , which is conserved throughout plant evolution, constitutes the first example of naturally occurring hydrolytic group II intron splicing in vivo .

During the period from sowing and planting to harvesting, outdoor crops are directly affected by the natural environment, including wind, rain, frost, and sunlight. Under such circumstances, vegetables change their growth conditions, shape, and flexibility daily. We aimed to develop an agricultural work-support robot that automates monitoring, cultivation, disease detection, and treatment. In recent years, many researchers and venture companies have developed agricultural harvesting robots. In this study, instead of focusing on intensive harvesting operations, we focused on daily farm operations from the beginning of cultivation to immediately before harvest. Therefore, gripping and cutting are considered basic functions that are common to several routine agricultural tasks. To find the assumed objects from a camera image with a low computational load, this study focuses on branch points to detect and identify even if the stems, lateral branches, and axillary buds are swaying in the wind. A branch point is a characteristic part close to the working position, even when the wind blows. Therefore, we propose a method to detect the assumed branch points simultaneously and divide each branch point into the main stem, lateral branch, and axillary bud. The effectiveness of this method is demonstrated through experimental evaluations using three types of vegetables, regardless of whether their stems are swaying.

Background Branch points (BPs) map within short motifs upstream of acceptor splice sites (3’ss) and are essential for splicing of pre-mature mRNA. Several BP-dedicated bioinformatics tools, including HSF, SVM-BPfinder, BPP, Branchpointer, LaBranchoR and RNABPS were developed during the last decade. Here, we evaluated their capability to detect the position of BPs, and also to predict the impact on splicing of variants occurring upstream of 3’ss. Results We used a large set of constitutive and alternative human 3’ss collected from Ensembl ( n  = 264,787 3’ss) and from in-house RNAseq experiments ( n  = 51,986 3’ss). We also gathered an unprecedented collection of functional splicing data for 120 variants (62 unpublished) occurring in BP areas of disease-causing genes. Branchpointer showed the best performance to detect the relevant BPs upstream of constitutive and alternative 3’ss (99.48 and 65.84% accuracies, respectively). For variants occurring in a BP area, BPP emerged as having the best performance to predict effects on mRNA splicing, with an accuracy of 89.17%. Conclusions Our investigations revealed that Branchpointer was optimal to detect BPs upstream of 3’ss, and that BPP was most relevant to predict splicing alteration due to variants in the BP area.

In this paper, we relate the theory of quasi-conformal maps to the regularity of the solutions to nonlinear thin-obstacle problems; we prove that the contact set is locally a finite union of intervals and apply this result to the solutions of one-phase Bernoulli free boundary problems with geometric constraint. We also introduce a new conformal hodograph transform, which allows to obtain the precise expansion at branch points of both the solutions to the one-phase problem with geometric constraint and a class of symmetric solutions to the two-phase problem, as well as to construct examples of free boundaries with cusp-like singularities.

Samples of two commercial low-density polyethylene melts were investigated with respect to their fracture behavior in controlled uniaxial extensional flow at constant strain rate in a filament stretching rheometer. In order to assess the possible influence of grain boundaries on fracture, the samples were prepared by three different types of pre-treatment: by compression molding of (1) virgin pellets used as received, (2) pellets homogenized in a twin-screw extruder, and (3) pellets that were milled into powder by cryogenic grinding under liquid nitrogen. The elongational stress growth data were analyzed by the Extended Hierarchical Multi-mode Molecular Stress Function (EHMMSF) model developed by Wagner et al. (Rheol. Acta 61, 281-298 (2022)) for long-chain branched (LCB) polymer melts. The EHMMSF model quantifies the elongational stress growth including the maximum in the elongational viscosity of LDPE melts based solely on the linear-viscoelastic relaxation spectrum and two nonlinear material parameters, the dilution modulus G D and a characteristic stretch parameter λ ¯ m . Within experimental accuracy, model predictions are in excellent agreement with the elongational stress growth data of the two LDPE melts, independent of the preparation method used. At sufficiently high strain rates, the fracture of the polymer filaments was observed and is in general accordance with the entropic fracture criterion implemented in the EHMMSF model. High-speed videography reveals that fracture is preceded by parabolic crack opening, which is characteristic for elastic fracture and which has been observed earlier in filament stretching of monodisperse polystyrene solutions. Here, for the first time, we demonstrate the appearance of a parabolic crack opening in the fracture process of polydisperse long-chain branched polyethylene melts.

Purpose To determine the multifractal and lacunarity characteristics of the retinal microvasculature in patients with migraine and compare with healthy controls. Methods A total of 112 eyes from 56 migraine patients (35 MWO, 21 MWA) and 102 eyes from 51 healthy controls were included in the study. Optical coherence tomography angiography (OCTA) was used to assess foveal and parafoveal vascular parameters. Vascular area density, vascular length density, vascular diameter index, vascular tortuosity, branch point density, non-flow area, and foveal avascular zone parameters were measured with ImageJ. Fractal dimensions (D₀, D₁, D₂), multifractal spectrum (D(q)), and lacunarity (parameter b ) were calculated using MATLAB. Results Migraine with aura patients showed significantly reduced vascular area density, vascular length density, vascular diameter index, and branch point density values, particularly in the deep capillary plexus. The foveal avascular zone area and perimeter were significantly enlarged in the migraine with aura group. Fractal analysis revealed a significant decrease in D₀, D₁, and D₂ values in migraine with aura, especially in the deep capillary plexus. The multifractal spectrum (D(q)) exhibited a consistent downward shift in migraine with aura, suggesting global architectural simplification. Although not statistically significant, lacunarity analysis showed a trend toward increased spatial heterogeneity in migraine with aura, reflected by lower b values. Conclusion Migraine, particularly with aura, is associated with reduced vascular complexity and increased spatial irregularity in the retinal microvasculature, especially at the level of the deep capillary plexus. Multifractal and lacunarity metrics may serve as sensitive indicators of subclinical microvascular disruption in migraine.

Obstructive pulmonary diseases are associated with considerable morbidity. For an early diagnosis of these diseases, inert gas washouts can potentially be used. However, the complex interaction between lung anatomy and gas transport mechanisms complicates data analysis. In order to investigate this interaction, a numerical model, based on the finite difference method, consisting of two lung units connected in parallel, was developed to simulate the tracer gas transport within the human acinus. Firstly, the geometries of the units were varied and the diffusion coefficients ( D ) were kept constant. Secondly, D was changed and the geometry was kept constant. Furthermore, simple monoexponential growth functions were applied to evaluate the simulated data. In 109 of the 112 analyzed curves, monoexponential function matched simulated data with an accuracy of over 90%, potentially representing a suitable numerical tool to predict transport processes in further model extensions. For total flows greater than 5 × 10 −4  ml/s, the exponential growth constants increased linearly with linear increasing flow to an accuracy of over 95%. The slopes of these linear trend lines of 1.23 µl −1 ( D  = 0.6 cm 2 /s), 1.69 µl −1 ( D  = 0.3 cm 2 /s), and 2.25 µl −1 ( D  = 0.1 cm 2 /s) indicated that gases with low D are more sensitive to changes in flows than gases with high D . Graphical abstract

We examine a free transmission problem driven by fully nonlinear elliptic operators. Since the transmission interface is determined endogenously, our analysis regards this object as a free boundary. We start by relating our problem with a pair of viscosity inequalities. Then, approximation methods ensure that strong solutions are of class C ^1,Log-Lip , locally. In addition, under further conditions on the problem, we prove quadratic growth of the solutions away from branch points.

Axonal varicosities or swellings are enlarged structures along axon shafts and profoundly affect action potential propagation and synaptic transmission. These structures, which are defined by morphology, are highly heterogeneous and often investigated concerning their roles in neuropathology, but why they are present in the normal brain remains unknown. Combining confocal microscopy and cryo-electron tomography (Cryo-ET) with in vivo and in vitro systems, we report that non-uniform mechanical interactions with the microenvironment can lead to 10-fold diameter differences within an axon of the central nervous system (CNS). In the brains of adult Thy1-YFP transgenic mice, individual axons in the cortex displayed significantly higher diameter variation than those in the corpus callosum. When being cultured on lacey carbon film-coated electron microscopy (EM) grids, CNS axons formed varicosities exclusively in holes and without microtubule (MT) breakage, and they contained mitochondria, multivesicular bodies (MVBs), and/or vesicles, similar to the axonal varicosities induced by mild fluid puffing. Moreover, enlarged axon branch points often contain MT free ends leading to the minor branch. When the axons were fasciculated by mimicking in vivo axonal bundles, their varicosity levels reduced. Taken together, our results have revealed the extrinsic regulation of the three-dimensional ultrastructures of central axons by the mechanical microenvironment under physiological conditions.

U2AF65 (U2AF2) and PUF60 (PUF60) are splicing factors important for recruitment of the U2 small nuclear ribonucleoprotein to lariat branch points and selection of 3′ splice sites (3′ss). Both proteins preferentially bind uridine-rich sequences upstream of 3′ss via their RNA recognition motifs (RRMs). Here, we examined 36 RRM substitutions reported in cancer patients to identify variants that alter 3′ss selection, RNA binding and protein properties. Employing PUF60- and U2AF65-dependent 3′ss previously identified by RNA-seq of depleted cells, we found that 43% (10/23) and 15% (2/13) of independent RRM mutations in U2AF65 and PUF60, respectively, conferred splicing defects. At least three RRM mutations increased skipping of internal U2AF2 (~9%, 2/23) or PUF60 (~8%, 1/13) exons, indicating that cancer-associated RRM mutations can have both cis- and trans-acting effects on splicing. We also report residues required for correct folding/stability of each protein and map functional RRM substitutions on to existing high-resolution structures of U2AF65 and PUF60. These results identify new RRM residues critical for 3′ss selection and provide relatively simple tools to detect clonal RRM mutations that enhance the mRNA isoform diversity.