Transmission Bottleneck Size Estimation from De Novo Viral Genetic Variation.

Sequencing of viral infections has become increasingly common over the last decade. Deep sequencing data in particular have proven useful in characterizing the roles that genetic drift and natural selection play in shaping within-host viral populations. They have also been used to estimate transmission bottleneck sizes from identified donor-recipient pairs. These bottleneck sizes quantify the number of viral particles that establish genetic lineages in the recipient host and are important to estimate due to their impact on viral evolution. Current approaches for estimating bottleneck sizes exclusively consider the subset of viral sites that are observed as polymorphic in the donor individual. However, these approaches have the potential to substantially underestimate true transmission bottleneck sizes. Here, we present a new statistical approach for instead estimating bottleneck sizes using patterns of viral genetic variation that arise de novo within a recipient individual. Specifically, our approach makes use of the number of clonal viral variants observed in a transmission pair, defined as the number of viral sites that are monomorphic in both the donor and the recipient but carry different alleles. We first test our approach on a simulated dataset and then apply it to both influenza A virus sequence data and SARS-CoV-2 sequence data from identified transmission pairs. Our results confirm the existence of extremely tight transmission bottlenecks for these 2 respiratory viruses.

Transcription factor PbNAC71 regulates xylem and vessel development to control plant height.

Dwarfism is an important agronomic trait in fruit breeding programs. However, the germplasm resources required to generate dwarf pear (Pyrus spp.) varieties are limited. Moreover, the mechanisms underlying dwarfism remain unclear. In this study, "Yunnan" quince (Cydonia oblonga Mill.) had a dwarfing effect on "Zaosu" pear. Additionally, the dwarfism-related NAC transcription factor gene PbNAC71 was isolated from pear trees comprising "Zaosu" (scion) grafted onto "Yunnan" quince (rootstock). Transgenic Nicotiana benthamiana and pear OHF-333 (Pyrus communis) plants overexpressing PbNAC71 exhibited dwarfism, with a substantially smaller xylem and vessel area relative to the wild-type controls. Yeast one-hybrid, dual-luciferase, chromatin immunoprecipitation-qPCR, and electrophoretic mobility shift assays indicated that PbNAC71 downregulates PbWalls are thin 1 expression by binding to NAC-binding elements in its promoter. Yeast two-hybrid assays showed that PbNAC71 interacts with the E3 ubiquitin ligase PbRING finger protein 217 (PbRNF217). Furthermore, PbRNF217 promotes the ubiquitin-mediated degradation of PbNAC71 by the 26S proteasome, thereby regulating plant height as well as xylem and vessel development. Our findings reveal a mechanism underlying pear dwarfism and expand our understanding of the molecular basis of dwarfism in woody plants.

[Study on methods measuring mechanical properties of arterial wall by macroscopic indentation].

Accurately evaluating the local biomechanics of arterial wall is crucial for diagnosing and treating arterial diseases. Indentation measurement can be used to evaluate the local mechanical properties of the artery. However, the effects of the indenter's geometric structure and the analysis theory on measurement results remain uncertain. In this paper, four kinds of indenters were used to measure the pulmonary aorta, the proximal thoracic aorta and the distal thoracic aorta in pigs, and the arterial elastic modulus was calculated by Sneddon and Sirghi theory to explore the influence of the indenter geometry and analysis theory on the measured elastic modulus. The results showed that the arterial elastic modulus measured by cylindrical indenter was lower than that measured by spherical indenter. In addition, compared with the calculated results of Sirghi theory, the Sneddon theory, which does not take adhesion forces in account, resulted in slightly larger elastic modulus values. In conclusion, this study provides parametric support for effective measurement of arterial local mechanical properties by millimeter indentation technique.

Instinct to insight: Neural correlates of ethological strategy learning.

In ethological behaviors like parenting, animals innately follow stereotyped patterns of choices to decide between uncertain outcomes but can learn to modify their strategies to incorporate new information. For example, female mice in a T-maze instinctively use spatial-memory to search for pups where they last found them but can learn more efficient strategies employing pup-associated acoustic cues. We uncovered neural correlates for transitioning between these innate and learned strategies. Auditory cortex (ACx) was required during learning. ACx firing at the nest increased with learning and correlated with subsequent search speed but not outcome. Surprisingly, ACx suppression rather than facilitation during search was more prognostic of correct sound-cued outcomes - even before adopting a sound-cued strategy. Meanwhile medial prefrontal cortex encoded the last pup location, but this decayed as the spatial-memory strategy declined. Our results suggest a neural competition between a weakening spatial-memory and strengthening sound-cued neural representation to mediate strategy switches.

Evaluating Short-Term and Long-Term Risks Associated with Renal Artery Stenosis Position and Severity: A Hemodynamic Study.

Background: Moderate renal artery stenosis (50-70%) may lead to uncontrolled hypertension and eventually cause irreversible damage to renal function. However, the clinical criteria for interventional treatment are still ambiguous in this condition. This study investigated the impact of the position and degree of renal artery stenosis on hemodynamics near the renal artery to assess the short-term and long-term risks associated with this disease. Methods: Calculation models with different degrees of stenosis (50%, 60%, and 70%) located at different positions in the right renal artery were established based on the computed tomography angiography (CTA) of a personalized case. And computational fluid dynamics (CFD) was used to analyze hemodynamic surroundings near the renal artery. Results: As the degree of stenosis increases and the stenosis position is far away from the aorta, there is a decrease in renal perfusion. An analysis of the wall shear stress (WSS)-related parameters indicated areas near the renal artery (downstream of the stenosis and the entrance of the right renal artery) with potential long-term risks of thrombosis and inflammation. Conclusion: The position and degree of stenosis play a significant role in judging short-term risks associated with renal perfusion. Moreover, clinicians should consider not only short-term risks but also independent long-term risk factors, such as certain regions of 50% stenosis with adequate renal perfusion may necessitate prompt intervention.

Impact of Cross-Limb Stent-Graft Configuration on Hemodynamics in Abdominal Aortic Aneurysm Interventional Therapy.

PURPOSE: The cross-limb (CL) technique is a commonly used endovascular treatment for addressing unfavorable anatomical features in patients with abdominal aortic aneurysm (AAA). The configuration of CL stent-graft plays a critical role in determining the postoperative hemodynamic properties and physiological behaviors, which ultimately impact the efficacy and safety of endovascular AAA treatment. This study aims to investigate the relationship between hemodynamics and CL stent-graft configuration from a hemodynamic perspective. METHODS: Five distinct geometric models of cross-limb (CL) stent-graft configurations were constructed by optimizing the real clinical computed tomography angiography (CTA) data. These models varied in main body lengths and cross angles and were used to perform numerical simulations to analyze various hemodynamic parameters. Flow pattern, distribution of wall shear stress (WSS)-related parameters, localized normalized helicity (LNH), pressure drop, and the displacement force of all models were examined in this paper. RESULTS: In patient-specific cases, helical flow and WSS increase with the main body. However, it also generated secondary flow in localized areas, leading to increased oscillation in the WSS direction. Notably, increasing the stent graft's main body length or decreasing the cross angle reduced the displacement force exerted on the stent-graft. Reducing the cross angle did not significantly alter the hemodynamic characteristics. CONCLUSION: In the clinical practice of CL deployment, it is crucial to carefully consider the stent-graft configuration and the patient specific to achieve optimal postoperative outcomes. This study provides valuable insights for guiding stent selection and treatment planning in patients with abdominal aortic aneurysm undergoing CL techniques, from a hemodynamic perspective.

Corneal Biomechanical Properties Demonstrate Anisotropy and Correlate With Axial Length in Myopic Eyes.

Purpose: The purpose of this study was to investigate the ex vivo and in vivo biomechanical characteristic of cornea in myopic eyes. Methods: Fifty-one corneal stromal lenticules were obtained from myopic eyes during the SMILE procedure and were tested by a biaxial tensile system within 24 hours postoperatively. The material properties of the lenticules were described using stress-strain curves and were compared among axial length (AL) <26 mm and AL ≥ 26 mm group. Pre-operative stress-strain index (SSI) parameters were used to evaluate the biomechanical properties of the cornea in vivo. Results: Compared with AL < 26 mm, the tangent modulus significantly decreased in horizontal and vertical directions when AL ≥ 26 mm (P < 0.05); SSI also significantly decreased when AL ≥ 26 mm (P < 0.05). Anisotropic parameter is positively correlated with AL (r = 0.307, P < 0.05). Compared with AL < 26 mm, anisotropic parameter significantly increased when AL ≥ 26 mm (P < 0.05). SSI was negatively correlated with AL (r = -0.380, P < 0.05) in the AL < 26 mm group but not in the AL ≥ 26 mm group (P > 0.05). Compared with 26 mm ≤ AL < 27 mm group, the tangent modulus significantly decreased in the horizontal direction (P < 0.05) but not in the vertical direction when 27 mm ≤ AL < 28 mm (P > 0.05). Conclusions: The biomechanical properties of cornea decreased with the increase of AL. Tangent modulus significantly decreased in the horizontal direction compared with vertical direction. AL should be taken into account during calculation of corneal biomechanical parameters in order to improve validity.