Discovery of Transacting Long Noncoding RNAs That Regulate Smooth Muscle Cell Phenotype.

BACKGROUND: Smooth muscle cells (SMC), the major cell type in atherosclerotic plaques, are vital in coronary artery diseases (CADs). SMC phenotypic transition, which leads to the formation of various cell types in atherosclerotic plaques, is regulated by a network of genetic and epigenetic mechanisms and governs the risk of disease. The involvement of long noncoding RNAs (lncRNAs) has been increasingly identified in cardiovascular disease. However, SMC lncRNAs have not been comprehensively characterized, and their regulatory role in SMC state transition remains unknown. METHODS: A discovery pipeline was constructed and applied to deeply strand-specific RNA sequencing from perturbed human coronary artery SMC with different disease-related stimuli, to allow for the detection of novel lncRNAs. The functional relevance of a select few novel lncRNAs were verified in vitro. RESULTS: We identified 4579 known and 13 655 de novo lncRNAs in human coronary artery SMC. Consistent with previous long noncoding RNA studies, these lncRNAs overall have fewer exons, are shorter in length than protein-coding genes (pcGenes), and have relatively low expression level. Genomic location of these long noncoding RNA is disproportionately enriched near CAD-related TFs (transcription factors), genetic loci, and gene regulators of SMC identity, suggesting the importance of their function in disease. Two de novo lncRNAs, ZIPPOR (ZEB-interacting suppressor) and TNS1-AS2 (TNS1-antisense 2), were identified by our screen. Combining transcriptional data and in silico modeling along with in vitro validation, we identified CAD gene ZEB2 as a target through which these lncRNAs exert their function in SMC phenotypic transition. CONCLUSIONS: Expression of a large and diverse set of lncRNAs in human coronary artery SMC are highly dynamic in response to CAD-related stimuli. The dynamic changes in expression of these lncRNAs correspond to alterations in transcriptional programs that are relevant to CAD, suggesting a critical role for lncRNAs in SMC phenotypic transition and human atherosclerotic disease.

Genome-Wide Genetic Associations Prioritize Evaluation of Causal Mechanisms of Atherosclerotic Disease Risk.

OBJECTIVE: The goal of this review is to discuss the implementation of genome-wide association studies to identify causal mechanisms of vascular disease risk. APPROACH AND RESULTS: The history of genome-wide association studies is described, the use of imputation and the creation of consortia to conduct meta-analyses with sufficient power to arrive at consistent associated loci for vascular disease. Genomic methods are described that allow the identification of causal variants and causal genes and how they impact the disease process. The power of single-cell analyses to promote genome-wide association studies of causal gene function is described. CONCLUSIONS: Genome-wide association studies represent a paradigm shift in the study of cardiovascular disease, providing identification of genes, cellular phenotypes, and disease pathways that empower the future of targeted drug development.

Extracellular vesicles from differentiated stem cells contain novel proangiogenic miRNAs and induce angiogenic responses at low doses.

Extracellular vesicles (EVs) released from healthy endothelial cells (ECs) have shown potential for promoting angiogenesis, but their therapeutic efficacy remains poorly understood. We have previously shown that transplantation of a human embryonic stem cell-derived endothelial cell product (hESC-ECP), promotes new vessel formation in acute ischemic disease in mice, likely via paracrine mechanism(s). Here, we demonstrated that EVs from hESC-ECPs (hESC-eEVs) significantly increased EC tube formation and wound closure in vitro at ultralow doses, whereas higher doses were ineffective. More important, EVs isolated from the mesodermal stage of the differentiation (hESC-mEVs) had no effect. Small RNA sequencing revealed that hESC-eEVs have a unique transcriptomic profile and are enriched in known proangiogenic microRNAs (miRNAs, miRs). Moreover, an in silico analysis identified three novel hESC-eEV-miRNAs with potential proangiogenic function. Differential expression analysis suggested that two of those, miR-4496 and miR-4691-5p, are highly enriched in hESC-eEVs. Overexpression of miR-4496 or miR-4691-5p resulted in increased EC tube formation and wound closure in vitro, validating the novel proangiogenic function of these miRNAs. In summary, we demonstrated that hESC-eEVs are potent inducers of EC angiogenic response at ultralow doses and contain a unique EV-associated miRNA repertoire, including miR-4496 and miR-4691-5p, with novel proangiogenic function.

Peptidoglycan synthesis drives an FtsZ-treadmilling-independent step of cytokinesis.

Peptidoglycan is the main component of the bacterial wall and protects cells from the mechanical stress that results from high intracellular turgor. Peptidoglycan biosynthesis is very similar in all bacteria; bacterial shapes are therefore mainly determined by the spatial and temporal regulation of peptidoglycan synthesis rather than by the chemical composition of peptidoglycan. The form of rod-shaped bacteria, such as Bacillus subtilis or Escherichia coli, is generated by the action of two peptidoglycan synthesis machineries that act at the septum and at the lateral wall in processes coordinated by the cytoskeletal proteins FtsZ and MreB, respectively. The tubulin homologue FtsZ is the first protein recruited to the division site, where it assembles in filaments-forming the Z ring-that undergo treadmilling and recruit later divisome proteins. The rate of treadmilling in B. subtilis controls the rates of both peptidoglycan synthesis and cell division. The actin homologue MreB forms discrete patches that move circumferentially around the cell in tracks perpendicular to the long axis of the cell, and organize the insertion of new cell wall during elongation. Cocci such as Staphylococcus aureus possess only one type of peptidoglycan synthesis machinery, which is diverted from the cell periphery to the septum in preparation for division. The molecular cue that coordinates this transition has remained elusive. Here we investigate the localization of S. aureus peptidoglycan biosynthesis proteins and show that the recruitment of the putative lipid II flippase MurJ to the septum, by the DivIB-DivIC-FtsL complex, drives peptidoglycan incorporation to the midcell. MurJ recruitment corresponds to a turning point in cytokinesis, which is slow and dependent on FtsZ treadmilling before MurJ arrival but becomes faster and independent of FtsZ treadmilling after peptidoglycan synthesis activity is directed to the septum, where it provides additional force for cell envelope constriction.

Marine Animal Co-Products-How Improving Their Use as Rich Sources of Health-Promoting Lipids Can Foster Sustainability.

Marine lipids are recognized for their-health promoting features, mainly for being the primary sources of omega-3 fatty acids, and are therefore critical for human nutrition in an age when the global supply for these nutrients is experiencing an unprecedent pressure due to an ever-increasing demand. The seafood industry originates a considerable yield of co-products worldwide that, while already explored for other purposes, remain mostly undervalued as sustainable sources of healthy lipids, often being explored for low-value oil production. These co-products are especially appealing as lipid sources since, besides the well-known nutritional upside of marine animal fat, which is particularly rich in omega-3 polyunsaturated fatty acids, they also have interesting bioactive properties, which may garner them further interest, not only as food, but also for other high-end applications. Besides the added value that these co-products may represent as valuable lipid sources, there is also the obvious ecological upside of reducing seafood industry waste. In this sense, repurposing these bioresources will contribute to a more sustainable use of marine animal food, reducing the strain on already heavily depleted seafood stocks. Therefore, untapping the potential of marine animal co-products as valuable lipid sources aligns with both health and environmental goals by guaranteeing additional sources of healthy lipids and promoting more eco-conscious practices.

Gelatin methacryloyl hydrogel with and without dental pulp stem cells for TMJ regeneration: An in vivo study in rabbits.

BACKGROUND: In the last decade, tissue-engineering strategies for regenerating the temporomandibular joint (TMJ) have been investigated. This may be a promising strategy for the minimally invasive restoration of joint integrity. OBJECTIVES: To evaluate whether dental pulp stem cells (DPSCs) loaded in a light-occured hydrogel made of gelatin methacryloyl (GelMA) enhance the regeneration of osteochondral defects in the rabbit TMJ. MATERIALS AND METHODS: Defects were filled with GelMA alone (control group; n = 4) or filled with GelMA loaded with rabbit DPSCs (experimental group; n = 4), In one group, the TMJ capsule was opened without creating a defect (sham group; n = 2). The following micro-CT parameters were analysed: bone volume to total volume ratio (BV/TV%) and bone mineral density (BMD). Histological evaluation was performed to assess cartilage regeneration features. A semi-quantitative scoring system was also used to evaluate the defects. RESULTS: All groups had no statistical difference regarding the micro-CT parameters. The highest mean healing score was found for the experimental group. After 4 weeks, there were no signs of hydrogel in either group or no signs of inflammation in the adjacent tissues. The tissue formed in the defect was dense fibrous connective tissue. CONCLUSION: Adding DPSCs to GelMA did not provide a regenerative enhancement in TMJ osteochondral defects. This resulted in similar micro-CT parameters after 4 weeks of healing, with improved signs of subchondral bone regeneration but no cartilage regeneration.

Revisiting thymic positive selection and the mature T cell repertoire for antigen.

To support effective host defense, the T cell repertoire must balance breadth of recognition with sensitivity for antigen. The concept that T lymphocytes are positively selected in the thymus is well established, but how this selection achieves such a repertoire has not been resolved. Here we suggest that it is direct linkage between self and foreign antigen recognition that produces the necessary blend of TCR diversity and specificity in the mature peripheral repertoire, enabling responses to a broad universe of unpredictable antigens while maintaining an adequate number of highly sensitive T cells in a population of limited size. Our analysis also helps to explain how diversity and frequency of antigen-reactive cells in a T cell repertoire are adjusted in animals of vastly different size scale to enable effective antipathogen responses and suggests a possible binary architecture in the TCR repertoire that is divided between germline-related optimal binding and diverse recognition.

MIR503HG Loss Promotes Endothelial-to-Mesenchymal Transition in Vascular Disease.

[Figure: see text].

A Framework for Representing, Building and Reusing Novel State-of-the-Art Three-Dimensional Object Detection Models in Point Clouds Targeting Self-Driving Applications.

The rapid development of deep learning has brought novel methodologies for 3D object detection using LiDAR sensing technology. These improvements in precision and inference speed performances lead to notable high performance and real-time inference, which is especially important for self-driving purposes. However, the developments carried by these approaches overwhelm the research process in this area since new methods, technologies and software versions lead to different project necessities, specifications and requirements. Moreover, the improvements brought by the new methods may be due to improvements in newer versions of deep learning frameworks and not just the novelty and innovation of the model architecture. Thus, it has become crucial to create a framework with the same software versions, specifications and requirements that accommodate all these methodologies and allow for the easy introduction of new methods and models. A framework is proposed that abstracts the implementation, reusing and building of novel methods and models. The main idea is to facilitate the representation of state-of-the-art (SoA) approaches and simultaneously encourage the implementation of new approaches by reusing, improving and innovating modules in the proposed framework, which has the same software specifications to allow for a fair comparison. This makes it possible to determine if the key innovation approach outperforms the current SoA by comparing models in a framework with the same software specifications and requirements.

Non-Destructive Inspection of High Temperature Piping Combining Ultrasound and Eddy Current Testing.

This paper presents an automated Non-Destructive Testing (NDT) system for the in-service inspection of orbital welds on tubular components operating at temperatures as high as 200 °C. The combination of two different NDT methods and respective inspection systems is here proposed to cover the detection of all potential defective weld conditions. The proposed NDT system combines ultrasounds and Eddy current techniques with dedicated approaches for dealing with high temperature conditions. Phased array ultrasound was employed, searching for volumetric defects within the weld bead volume while Eddy currents were used to look for surface and sub-surface cracks. The results from the phased array ultrasound results showed the effectiveness of the cooling mechanisms and that temperature effects on sound attenuation can be easily compensated for up to 200 °C. The Eddy current results showed almost no influence when temperatures were raised up to 300 °C.

Implementation, Reach, and Effectiveness of the Direct Observation of Residents in Clinic Program.

BACKGROUND: Direct observation is important, yet medical residents are rarely observed. We implemented and evaluated a direct observation program in resident clinics to increase the frequency of observation and feedback and improve perceptions about direct observation. METHODS: We assigned faculty as observers in our resident clinics between June 2019 and February 2020. We surveyed residents and faculty before and after the program. Faculty completed a form for each observation performed. We analyzed surveys to examine changes in barriers, frequency and type of observations and feedback, and attitudes toward observation. The analytical sample included 38 and 37 pre- and postresident surveys, respectively, and 20 and 25 pre- and postfaculty surveys, respectively. RESULTS: Resident survey response rates were 32.3% (40/124) pre- and 30.7% (39/127) postintervention. Most residents (76% [pre], 86% [post], P = 0.258) reported being observed in at least one of the four areas: history, examination, counseling, or wrap-up. We received observation tracking forms on 68% of eligible residents. Observed history taking increased from 30% to 79% after the program (P = 0.0010). Survey response rates for faculty were 64.7% (22/34) pre- and 67.5% (25/37) postintervention. Fewer faculty reported time (80% [pre], 52% [post], P = 0.051) and competing demands (65% [pre], 52% [post], P = 0.380) as barriers postintervention. Fewer faculty postintervention viewed observation as a valuable teaching tool (100% [pre], 79% [post], P = 0.0534). All faculty who did not view observation as valuable were the least experienced. DISCUSSION: Assigning faculty as observers can increase observation, especially in history taking, though data suggest an increase in negative perceptions of observation by faculty.

Clinical comparison of conventional suture and tissue adhesive in third molar surgeries: a systematic review.

The use of cyanoacrylate tissue adhesive for surgical wound closure has become increasingly popular in recent years and has shown efficacy. Therefore, the aim of this systematic review was to compare the effectiveness of cyanoacrylate adhesive as a substitute for conventional suture placement after extraction of impacted third molars. The PubMed/MEDLINE, Scopus, Cochrane, and gray literature databases were searched for randomized or controlled prospective clinical trials published up to October 2022 that compared the use of cyanoacrylate adhesive and conventional silk suture in third molar surgeries. The risk of bias of each study was assessed using the RoB 2 tool (revised Cochrane risk of bias tool for randomized trials). Five randomized clinical trials with a total of 236 patients were included. The most commonly evaluated outcomes were pain and bleeding. The type of adhesive used varied and included ethyl-2-cyanoacrylate, isoamyl 2-cyanoacrylate, and a mixture of n-butyl cyanoacrylate and 2-octyl cyanoacrylate. Compared with 3-0 silk suture, cyanoacrylate tissue adhesive resulted in lower levels of postoperative pain in 3 studies and lower rates of bleeding in all 5 studies. Thus, cyanoacrylate can be a good substitute for silk sutures for wound closure in intraoral surgeries.

Revisiting the Role of VraTSR in Staphylococcus aureus Response to Cell Wall-Targeting Antibiotics.

Exposure of Staphylococcus aureus to cell wall inhibitors leads to the activation of the VraTSR three-component sensory regulatory system. This system is composed of VraS, a membrane histidine kinase; VraR, its cognate response regulator, and VraT, a protein required for the full activity of VraTSR. The exact function of VraT remains mostly uncharacterized, although it has been proposed to detect the unknown stimulus sensed by the VraTSR system. Here, we elucidate the topology of VraT, showing that its C-terminal domain is extracellular. We also demonstrate that the signal sensed by VraTSR is not an intermediate in the peptidoglycan synthesis pathway, as previously suggested. Instead, the specific inhibition of the penicillin-binding protein (PBP)2 leads to strong activation of the system. IMPORTANCE The Gram-positive bacterial pathogen Staphylococcus aureus is currently the second most frequent cause of global deaths associated with antibiotic resistance. Its response to cell wall-targeting antibiotics requires the VraTSR three-component system, which senses cell wall damage. Here, we show that the signal sensed by VraTSR is not an intermediate in the peptidoglycan synthesis pathway, as previously suggested. Instead, the specific inhibition of the penicillin-binding protein (PBP)2, the major peptidoglycan synthase in S. aureus, leads to strong activation of the system. Identifying the exact cell wall damage signal is key to fully understanding the response of S. aureus to cell wall-targeting antibiotics.

T cell-positive selection uses self-ligand binding strength to optimize repertoire recognition of foreign antigens.

Developing T cells express diverse antigen receptors whose specificities are not prematched to the foreign antigens they eventually encounter. Past experiments have revealed that thymocytes must productively signal in response to self antigens to mature and enter the peripheral T cell pool (positive selection), but how this process enhances effective mature T cell responses to foreign antigen is not fully understood. Here we have documented an unsuspected connection between thymic recognition events and foreign antigen-driven T cell responses. We find that the strength of self-reactivity is a clone-specific property unexpectedly directly related to the strength of T cell receptor (TCR) binding to presented foreign antigen. T cells with receptors showing stronger interaction with self dominate in responses to infections and accumulate in aging individuals, revealing that positive selection contributes to effective immunity by skewing the mature TCR repertoire toward highly effective recognition of pathogens that pose a danger to the host.

Analysis of Decreasing Adverse Events with Endoscopic Ultrasound in a New Advanced Endoscopy Program Over Time.

OBJECTIVE: New innovations and increasing utility of endoscopic ultrasound (EUS) are associated with rare but serious risks. We investigate the rates and risk factors for post-procedural complications over a four-year period at a new advanced endoscopy program. METHODS: We conducted a retrospective review of all adult patients who underwent upper EUS at an academic level-1 trauma center between April 2015 and November 2019. The primary outcome was the incidence of adverse events within 1 week of EUS. Secondary outcomes included emergency department visits and mortality within 30 days after EUS. Chi-square test, t test, and multivariable logistic regression were used to assess risk factors for post-procedural complications. RESULTS: A total of 968 EUS procedures were performed on 864 patients (54% female; 79% Caucasian; mean age 61 years). The overall incidence of post-procedural adverse event with EUS was 5.6%. The probability of an adverse event decreased by an average of 22% per year (p =0.01, OR 0.78). The risk for adverse events were 3.3% acute pancreatitis, 1.9% clinically significant bleeding, 0.3% bacteremia, 0.2% perforation, and 2.4% 30-day mortality. The adverse event rate was highest among low volume proceduralists (p =0.04). The 30-day mortality was more than threefolds among patients who had an adverse event within 7 days after EUS. CONCLUSION: The overall incidence of post-procedural adverse events at a new EUS program was 5.6%, with an average of 22% relative decrease in adverse events per year in the first 4 years.

Temperature and pressure dependent rate constants of the reactions of OH• with cyclopentene from variational TST and SS-QRRK methods.

In this work, the pressure- and temperature-dependent reaction rate constants for the hydrogen abstraction and addition of hydroxyl radicals to the unsaturated cyclopentene were studied. Geometries and vibrational frequencies of reactants, products, and transition states were calculated using density functional theory, with single-point energy corrections determined at the domain-based local pair natural orbital-coupled-cluster single double triple/cc-pVTZ-F12 level. The high-pressure limit rate constants were calculated using the canonical variational transition state theory with the small-curvature tunneling approximation. The vibrational partition functions were corrected by the effects of torsional and ring-puckering anharmonicities of the transition states and cyclopentene, respectively. Variational effects are shown to be relevant for all the hydrogen abstraction reactions. The increasing of the rate constants by tunneling is significant at temperatures below 500 K. The pressure dependence on the rate constants of the addition of OH• to cyclopentene was calculated using the system-specific quantum Rice-Ramsperger-Kassel model. The high-pressure limit rate constants decrease with increasing temperature in the range 250-1000 K. The falloff behavior was studied at several temperatures with pressures varying between 10-3 and 103 bar. At temperatures below 500 K, the effect of the pressure on the addition rate constant is very modest. However, at temperatures around and above 1000 K, taking pressure into account is mandatory for an accurate rate constant calculation. Branching ratio analyses reveal that the addition reaction dominates at temperatures below 500 K, decreasing rapidly at higher temperatures. Arrhenius parameters are provided for all reactions and pressure dependent Arrhenius parameters are given for the addition of OH• to cyclopentene.

IRIS: Infection with RespIratory Syncytial Virus in infants-a prospective observational cohort study.

BACKGROUND: Respiratory syncytial virus (RSV) is the most common cause of acute lower respiratory tract infection in infants. Globally, RSV is responsible for approximately 3.2 million hospital admissions and about 60,000 in-hospital deaths per year. METHODS: Infection with RespIratory Syncytial Virus (IRIS) is an observational, multi-centre study enrolling infants with severe RSV infection and healthy controls. Inclusion criteria are age between 0 and 36 months and hospitalisation due to RSV infection at three German sites. Exclusion criteria are premature birth, congenital or acquired bronchopulmonary or cardiac diseases, and immunodeficiency. Healthy control probands are enrolled via recruitment of patients undergoing routine surgical procedures. Blood and respiratory specimens are collected upon admission, and RSV and other pathogens are analysed by multiplex polymerase chain reaction. Different biomaterials, including plasma, nasal lining fluid, blood cells, DNA, and RNA specimens, are sampled in a dedicated biobank. Detailed information on demographic characteristics and medical history is recorded, and comprehensive clinical data, including vital signs, medication, and interventions. DISCUSSION: The IRIS study aims to discover host and viral factors controlling RSV disease courses in infants. The approach including multi-omics characterisation in clinically well-characterized children with RSV bronchiolitis seeks to improve our understanding of the immune response against this virus. It may disclose novel diagnostic and treatment approaches for respiratory infections in infants. TRIAL REGISTRATION: ClinicalTrials.gov, NCT04925310. Registered 01 October 2021-Retrospectively registered. https://clinicaltrials.gov/ct2/show/NCT04925310?cond=NCT04925310&draw=2&rank=1.