Search

Biotechnological processes are essential for developing economies that aim to stand out in future markets. The use of bioreactors is one of the most important unit operations of biotechnological processes, and real-time monitoring of bioreactors is essential to ensure precise bioprocess control. This review presents different types of bioreactors, sensors, and applications in other sectors. Bioreactors, controlled systems for cultivating microorganisms and cells, are essential tools in various fields, from scientific research to industrial production. The use of a variety of sensors is critical for accurate, real-time monitoring, early problem detection, reproducibility, cost reduction, and increased efficiency. These benefits are being realized in numerous applications, including biofuel production, bioremediation and leaching processes, tissue engineering, and drug manufacturing. Innovations in bioreactor technology are expanding opportunities for a more sustainable and healthier future. By developing new types of bioreactors, integrating advanced sensors, and exploring promising applications, bioreactors are playing a key role in addressing global challenges and sustainably advancing science and technology.

Two cross-modal naming experiments examined the role of working memory in processing sentences and discourses of various lengths. In Experiment 1, 10 memory impaired patients with probable Alzheimer's disease (AD) and 10 healthy elderly control participants showed similar sensitivity to violations of subject-verb number agreement in a short sentence condition and similar degradation to this sensitivity in a long sentence condition. Performance in neither length condition correlated with performance on working memory tasks, suggesting that the processes involved in interpreting a grammatical dependency between adjacent and nonadjacent elements are different from those required in the working memory tasks. In Experiment 2, the same 10 AD patients were less sensitive than the 10 control participants to pronoun-antecedent number agreement violations in a short discourse condition, but neither group was affected by additional length. In this experiment, performance in both the short and long conditions correlated with working memory performance. These results show that grammatical and discourse dependencies pose different memory and processing demands, and that these differences are not simply due to differences in the amount of intervening material between dependent words. The results also suggest that while the working memory deficits characteristic of AD do not interfere with on-line grammatical processing within sentences, they do compromise on-line discourse processing across sentences. [ABSTRACT FROM AUTHOR]

Aim: Gestational diabetes mellitus (GDM) has been associated with reduced postprandial glucagon-like peptide 1 (GLP-1) responses. As pregnancy induces changes in gallbladder motility and bile acids stimulate GLP-1 secretion, we investigated postprandial gallbladder emptying and GLP-1 responses in women with GDM., Methods: Women with and without GDM underwent two 240-min mixed meal tests; one during third trimester of pregnancy and one 3-6 months postpartum. We evaluated ultrasonography-assessed gallbladder emptying, plasma concentrations of glucometabolic hormones including GLP-1, paracetamol absorption (proxy for gastric emptying) and circulating factors known to affect gallbladder dynamics., Results: Fifteen women with GDM and 15 pregnant women with normal glucose tolerance (NGT) (baseline median age 31 (interquartile range 29;33) versus 32 (28;33) years, body mass index (BMI) 27.2 (24.7;30.7) versus 28.4 (26.2;31.0) kg/m 2 , HbA 1c 30 (29;32) versus 30 (28;31) mmol/mol) were included. No differences in postprandial gallbladder emptying or GLP-1 responses were observed between women with and without GDM, neither during pregnancy nor postpartum. Pregnancy increased fasting gallbladder volumes by 69 (30;122)% and 103 (59;156)% and postprandial gallbladder emptying by 77 (28;236)% and 99 (37;190)% compared with postpartum in women with and without GDM, respectively. Postprandial GLP-1 responses were reduced by 60 (3;82)% and 81 (11;90)% during pregnancy compared with postpartum in women with and without GDM, respectively., Conclusion: Pregnancy-induced changes in gallbladder motility seem to play no or a limited role in previously reported GDM-associated reduced postprandial GLP-1 responses as gallbladder emptying was greater and postprandial GLP-1 response was lower in pregnancy than postpartum regardless of GDM status., (© 2024 John Wiley & Sons Ltd.)

Large-scale and continuous conformational changes in the RNA self-folding process present significant challenges for structural studies, often requiring trade-offs between resolution and observational scope. Here, we utilize individual-particle cryo-electron tomography (IPET) to examine the post-transcriptional self-folding process of designed RNA origami 6-helix bundle with a clasp helix (6HBC). By avoiding selection, classification, averaging, or chemical fixation and optimizing cryo-ET data acquisition parameters, we reconstruct 120 three-dimensional (3D) density maps from 120 individual particles at an electron dose of no more than 168 e - Å -2 , achieving averaged resolutions ranging from 23 to 35 Å, as estimated by Fourier shell correlation (FSC) at 0.5. Each map allows us to identify distinct RNA helices and determine a unique tertiary structure. Statistical analysis of these 120 structures confirms two reported conformations and reveals a range of kinetically trapped, intermediate, and highly compacted states, demonstrating a maturation folding landscape likely driven by helix-helix compaction interactions., (© 2024. The Author(s).)

Gene synthesis efficiency has greatly improved in recent years but is limited when it comes to repetitive sequences and results in synthesis failure or delays by DNA synthesis vendors. Here, we describe a method for the assembly of small synthetic genes with repetitive elements: First, a gene of interest is split in silico into small synthons of up to 80 base pairs flanked by Golden Gate-compatible overhangs. Then synthons are made by oligo extension and finally assembled into a synthetic gene by Golden Gate assembly., (© 2025. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Atraumatic soft issue handling is essential for optimal wound healing. Simulation is a safe and effective way to improve surgical skills outside the operating room. Our primary aim was the development of a pressure-sensing forceps that measures the force applied to a given tissue and provides real-time biofeedback. Seventy-eight students and trainees performed four trials of a continuous subcuticular closure using our Tissue Handling Trainer System device on a silicone skin model. We recorded the occurrence of above-threshold pressure and duration of time over the threshold. A one-way analysis of variance with Tukey post hoc test was used to analyze duration above-threshold pressure. There were statistically significant differences in the duration above threshold from trials 1 to 3 ( P < 0.001). A 36% reduction occurred between trials 1 and 2 after participants learned of the study purpose, but a 70% reduction between trials 2 and 3 with audible feedback. There was no statistically significant difference between trials 3 and 4 ( P = 0.807). The Tissue Handling Trainer System may be an effective technique for improving tissue handling skills in the surgical simulation laboratory., Competing Interests: The authors have no financial interest to declare in relation to the content of this article., (Copyright © 2024 The Authors. Published by Wolters Kluwer Health, Inc. on behalf of The American Society of Plastic Surgeons.)

Diagnosing patients in the medical emergency department is complex and this is expected to increase in many countries due to an ageing population. In this study we investigate the feasibility of training machine learning algorithms to assist physicians handling the complex situation in the medical emergency departments. This is expected to reduce diagnostic errors and improve patient logistics and outcome. We included a total of 9,190 consecutive patient admissions diagnosed and treated in two hospitals in this cohort study. Patients had a biochemical workup including blood and urine analyses on clinical decision totaling 260 analyses. After adding nurse-registered data we trained 19 machine learning algorithms on a random 80% sample of the patients and validated the results on the remaining 20%. We trained algorithms for 19 different patient outcomes including the main outcomes death in 7 (Area under the Curve (AUC) 91.4%) and 30 days (AUC 91.3%) and safe-discharge(AUC 87.3%). The various algorithms obtained areas under the Receiver Operating Characteristics -curves in the range of 71.8-96.3% in the holdout cohort (68.3-98.2% in the training cohort). Performing this list of biochemical analyses at admission also reduced the number of subsequent venipunctures within 24 h from patient admittance by 22%. We have shown that it is possible to develop a list of machine-learning algorithms with high AUC for use in medical emergency departments. Moreover, the study showed that it is possible to reduce the number of venipunctures in this cohort., (© 2024. The Author(s).)

Community-acquired pneumonia is a common cause of acute hospitalisation. Identifying patients with community-acquired pneumonia among patients suspected of having the disease can be a challenge, which causes unnecessary antibiotic treatment. We investigated whether the circulatory pulmonary injury markers surfactant protein D (SP-D), Krebs von den Lungen-6 (KL-6), and Club cell protein 16 (CC16) could help identify patients with community-acquired pneumonia upon acute admission. In this multi-centre diagnostic accuracy study, SP-D, KL-6, and CC16 were quantified in plasma samples from acutely hospitalised patients with provisional diagnoses of community-acquired pneumonia. The area under the receiver operator characteristics curve (AUC) was calculated for each marker against the following outcomes: patients' final diagnoses regarding community-acquired pneumonia assigned by an expert panel, and pneumonic findings on chest CTs. Plasma samples from 339 patients were analysed. The prevalence of community-acquired pneumonia was 63%. AUCs for each marker against both final diagnoses and chest CT diagnoses ranged between 0.50 and 0.56. Thus, SP-D, KL-6, and CC16 demonstrated poor diagnostic performance for community-acquired pneumonia in acutely hospitalised patients. Our findings indicate that the markers cannot readily assist physicians in confirming or ruling out community-acquired pneumonia.

Background: Artificial intelligence models constitute specific uses of analysis results and, therefore, necessitate evaluation of analytical performance specifications (APS) for this context specifically. The Model of End-stage Liver Disease (MELD) is a clinical prediction model based on measurements of bilirubin, creatinine, and the international normalized ratio (INR). This study evaluates the propagation of error through the MELD, to inform choice of APS for the MELD input variables., Methods: A total of 6093 consecutive MELD scores and underlying analysis results were retrospectively collected. "Desirable analytical variation" based on biological variation as well as current local analytical variation was simulated onto the data set as well as onto a constructed data set, representing a worst-case scenario. Resulting changes in MELD score and risk classification were calculated., Results: Biological variation-based APS in the worst-case scenario resulted in 3.26% of scores changing by ≥1 MELD point. In the patient-derived data set, the same variation resulted in 0.92% of samples changing by ≥1 MELD point, and 5.5% of samples changing risk category. Local analytical performance resulted in lower reclassification rates., Conclusions: Error propagation through MELD is complex and includes population-dependent mechanisms. Biological variation-derived APS were acceptable for all uses of the MELD score. Other combinations of APS can yield equally acceptable results. This analysis exemplifies how error propagation through artificial intelligence models can become highly complex. This complexity will necessitate that both model suppliers and clinical laboratories address analytical performance specifications for the specific use case, as these may differ from performance specifications for traditional use of the analyses., (© Association for Diagnostics & Laboratory Medicine 2024. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

RNA nanotechnology aims to use RNA as a programmable material to create self-assembling nanodevices for application in medicine and synthetic biology. The main challenge is to develop advanced RNA robotic devices that both sense, compute, and actuate to obtain enhanced control over molecular processes. Here, we use the RNA origami method to prototype an RNA robotic device, named the "Traptamer," that mechanically traps the fluorescent aptamer, iSpinach. The Traptamer is shown to sense two RNA key strands, acts as a Boolean AND gate, and reversibly controls the fluorescence of the iSpinach aptamer. Cryo-electron microscopy of the closed Traptamer structure at 5.45-angstrom resolution reveals the mechanical mode of distortion of the iSpinach motif. Our study suggests a general approach to distorting RNA motifs and a path forward to build sophisticated RNA machines that through sensing, computing, and actuation modules can be used to precisely control RNA functionalities in cellular systems.

Background : Urinary tract infections (UTIs) are a leading bacterial infection in the emergency department (ED). Diagnosing UTIs in the ED can be challenging due to the heterogeneous presentation; therefore, fast and precise tests are needed. We aimed to evaluate the diagnostic precision of procalcitonin (PCT), soluble urokinase plasminogen activator receptors (suPARs), and C-reactive protein (CRP) in diagnosing UTIs, grading the severity of UTIs, and ruling out bacteremia. Methods : We recruited adults admitted to three Danish EDs with suspected UTIs. PCT, suPAR, and CRP were used in index tests, while blood cultures, expert panel diagnosis, and severity grading were used in the reference tests. Logistic regression and area under the receiver operator characteristic curves (AUROCs) were utilized to evaluate the models and determine the optimal cut-offs. Results : We enrolled 229 patients. PCT diagnosed UTI with an AUROC of 0.612, detected severe disease with an AUROC of 0.712, and ruled out bacteremia with an AUROC of 0.777. SuPAR had AUROCs of 0.480, 0.638, and 0.605, while CRP had AUROCs of 0.599, 0.778, and 0.646. Conclusions : The diagnostic performance of PCT, suPAR, or CRP for UTIs or to rule out severe disease was poor. However, PCT can safely rule out bacteremia in clinically relevant numbers in ED patients suspected of UTI.

Gene synthesis efficiency has greatly improved in recent years but is limited when it comes to repetitive sequences, which results in synthesis failure or delays by DNA synthesis vendors. This represents a major obstacle for the development of synthetic biology since repetitive elements are increasingly being used in the design of genetic circuits and design of biomolecular nanostructures. Here, we describe a method for the assembly of small synthetic genes with repetitive elements: First, a gene of interest is split in silico into small synthons of up to 80 base pairs flanked by Golden-Gate-compatible overhangs. Then, synthons are made by oligo extension and finally assembled into a synthetic gene by Golden Gate Assembly. We demonstrate the method by constructing eight challenging genes with repetitive elements, e.g., multiple repeats of RNA aptamers and RNA origami scaffolds with multiple identical aptamers. The genes range in size from 133 to 456 base pairs and are assembled with fidelities of up to 87.5%. The method was developed to facilitate our own specific research but may be of general use for constructing challenging and repetitive genes and, thus, a valuable addition to the molecular cloning toolbox.

Water is one of the most reactive and abundant molecules on Earth, and it is thus crucial to understand its reactivity with various material families. One of the big unknown questions is how water in liquid and vapor forms impact the fast-emerging class of metal-organic frameworks (MOFs). Here, we discover that high-pressure water vapor drastically modifies the structure and hence the dynamic, thermodynamic, and mechanical properties of MOF glasses. In detail, we find that an archetypical MOF (ZIF-62) is extremely sensitive to heat treatments performed at 460 °C and water vapor pressures up to ∼110 bar. Both the melting and glass transition temperatures decrease remarkably (by >100 °C), and simultaneously, hardness and Young's modulus increase by up to 100% under very mild treatment conditions (<20 bar of hydrothermal pressure). Structural analyses suggest water to partially coordinate to Zn in the form of a hydroxide ion by replacing a bridging imidazolate-based linker. The work provides insight into the role of hot-compressed water in influencing the structure and properties of MOF glasses and opens a new route for systematically changing the thermodynamics and kinetics of MOF liquids and thus altering the thermal and mechanical properties of the resulting MOF glasses., Competing Interests: The authors declare no competing financial interest., (© 2024 The Authors. Published by American Chemical Society.)

Objective: The objective of this scoping review is to describe the scope and nature of research on the monitoring of clinical artificial intelligence (AI) systems. The review will identify the various methodologies used to monitor clinical AI, while also mapping the factors that influence the selection of monitoring approaches., Introduction: AI is being used in clinical decision-making at an increasing rate. While much attention has been directed toward the development and validation of AI for clinical applications, the practical implementation aspects, notably the establishment of rational monitoring/quality assurance systems, has received comparatively limited scientific interest. Given the scarcity of evidence and the heterogeneity of methodologies used in this domain, there is a compelling rationale for conducting a scoping review on this subject., Inclusion Criteria: This scoping review will include any publications that describe systematic, continuous, or repeated initiatives that evaluate or predict clinical performance of AI models with direct implications for the management of patients in any segment of the health care system., Methods: Publications will be identified through searches of the MEDLINE (Ovid), Embase (Ovid), and Scopus databases. Additionally, backward and forward citation searches, as well as a thorough investigation of gray literature, will be conducted. Title and abstract screening, full-text evaluation, and data extraction will be performed by 2 or more independent reviewers. Data will be extracted using a tool developed by the authors. The results will be presented graphically and narratively., Review Registration: Open Science Framework https://osf.io/afkrn., Competing Interests: The authors declare no conflicts of interest., (Copyright © 2024 JBI.)

Urinary tract infections (UTIs) are a leading infectious cause of emergency department admission. Early UTI diagnosis is challenging, and a faster, preferably point-of-care urine analysis is necessary. We aimed to evaluate the diagnostic accuracy of urine flow cytometry (UFC) and urine dipstick analysis (UDA) in identifying bacteriuria and UTIs. This study included adults suspected of an infection admitted to three Danish emergency departments. UFC and UDA were the index tests, and urine culture and an expert panel diagnosis were the reference tests. We used logistic regression and receiver operator characteristics curves to find each test's optimal model and cut-off. We enrolled 966 patients and performed urine cultures on 786. Urine culture was positive in 337, and 200 patients were diagnosed with a UTI. The UFC model ruled out bacteriuria in 10.9% with a negative predictive value (NPV) of 94.6% and ruled out UTI in 38.6% with an NPV of 97.0%. UDA ruled out bacteriuria in 52.1% with an NPV of 79.2% and UTI in 52.8% with an NPV of 93.9%. Neither UFC nor UDA performed well in ruling out bacteriuria in our population. In contrast, both tests ruled out UTI safely and in clinically relevant numbers.

The emergence of an RNA replicase capable of self-replication is considered an important stage in the origin of life. RNA polymerase ribozymes (PR) - including a variant that uses trinucleotide triphosphates (triplets) as substrates - have been created by in vitro evolution and are the closest functional analogues of the replicase, but the structural basis for their function is poorly understood. Here we use single-particle cryogenic electron microscopy (cryo-EM) and high-throughput mutation analysis to obtain the structure of a triplet polymerase ribozyme (TPR) apoenzyme and map its functional landscape. The cryo-EM structure at 5-Å resolution reveals the TPR as an RNA heterodimer comprising a catalytic subunit and a noncatalytic, auxiliary subunit, resembling the shape of a left hand with thumb and fingers at a 70° angle. The two subunits are connected by two distinct kissing-loop (KL) interactions that are essential for polymerase function. Our combined structural and functional data suggest a model for templated RNA synthesis by the TPR holoenzyme, whereby heterodimer formation and KL interactions preorganize the TPR for optimal primer-template duplex binding, triplet substrate discrimination, and templated RNA synthesis. These results provide a better understanding of TPR structure and function and should aid the engineering of more efficient PRs., Competing Interests: Competing interests statement:The authors declare no competing interest.

Aim: We investigated the effect of 52-week treatment with liraglutide, a glucagon-like peptide 1 receptor agonist, on glucose tolerance and incretin effect in women with previous gestational diabetes mellitus (pGDM)., Materials and Methods: Women with overweight/obesity and pGDM were randomized to once daily subcutaneous liraglutide 1.8 mg or placebo for 52 weeks. Participants underwent oral glucose tolerance test (OGTT) and isoglycaemic intravenous glucose infusion at baseline and at 52 weeks, and an additional OGTT after the drug wash-out., Results: In total, 104 women [age: mean ± SD, 38 ± 5 years; fasting plasma glucose (FPG): 5.5 ± 0.4 mmol/L; glycated haemoglobin (HbA1c): 33 ± 4 mmol/mol, bodyweight: 88.2 ± 14.8 kg, body mass index: 31.1 ± 4.3 kg/m 2 ] were assigned to liraglutide (n = 49) or placebo (n = 55). Estimated treatment difference (ETD) for area under curve during OGTT was -173 (95% confidence interval -250 to -97) mmol/L × min, p < .0001, but after wash-out the difference disappeared [ETD 58 (-30 to 146) mmol/L × min, p = .536]. Liraglutide reduced FPG [ETD -0.2 (-0.4 to -0.1) mmol/L, p = .018], HbA1c [-2.2 (-3.5 to -0.8) mmol/mol, p = .018] and bodyweight [-3.9 (-6.2 to -1.6) kg, p = .012]. No change in the incretin effect was observed. The number of women with prediabetes was reduced from 64% to 10% with liraglutide vs. 50% with placebo [adjusted odds ratio 0.10 (0.03-0.32), p = .002]., Conclusions: Treatment with liraglutide for 52 weeks improved glucose tolerance, FPG, HbA1c and bodyweight in women with overweight/obesity and pGDM. Progression to prediabetes while on drug was markedly reduced, but after a 1-week drug wash-out, the effect was lost., (© 2023 John Wiley & Sons Ltd.)

Background: Infection following implant-based breast reconstruction can lead to devastating complications. Risk factors for infection include smoking, diabetes, and obesity. Intraoperative hypothermia may represent another modifiable risk factor. This study analyzed the effect of hypothermia in postmastectomy immediate implant-based reconstruction on postoperative surgical-site infection (SSI)., Methods: This was a retrospective review of 122 patients with intraoperative hypothermia, defined as less than 35.5°C, and 106 normothermic patients who underwent postmastectomy implant-based reconstruction between 2015 and 2021. Demographics, comorbidities, smoking status, hypothermia (and its duration), and length of surgery were collected. The primary outcome was SSI. Secondary outcomes included reoperation and delayed wound healing., Results: A total of 185 patients (81%) underwent staged reconstruction with tissue expander placement and 43 patients (18.9%) had a direct-to-implant procedure. Over half (53%) of the patients experienced intraoperative hypothermia. In the hypothermic group, a higher proportion of patients had SSIs (34.4% versus 17% of normothermic patients; P < 0.05) and wound healing complications (27.9% versus 16%; P < 0.05). Intraoperative hypothermia predicted SSI (OR, 2.567; 95% CI, 1.367 to 4.818; P < 0.05) and delayed wound healing (OR, 2.023; 95% CI, 1.053 to 3.884; P < 0.05). Longer duration of hypothermia significantly correlated with SSI, with an average 103 minutes versus 77 minutes ( P < 0.05)., Conclusions: This study demonstrates that intraoperative hypothermia is a significant risk factor for postoperative infection in postmastectomy implant-based breast reconstruction. Maintaining strict normothermia during implant-based breast reconstruction procedures may improve patient outcomes by reducing the risk of postoperative infection and delayed wound healing., Clinical Question/level of Evidence: Risk, II., (Copyright © 2023 by the American Society of Plastic Surgeons.)

The first RNA category of the Critical Assessment of Techniques for Structure Prediction competition was only made possible because of the scientists who provided experimental structures to challenge the predictors. In this article, these scientists offer a unique and valuable analysis of both the successes and areas for improvement in the predicted models. All 10 RNA-only targets yielded predictions topologically similar to experimentally determined structures. For one target, experimentalists were able to phase their x-ray diffraction data by molecular replacement, showing a potential application of structure predictions for RNA structural biologists. Recommended areas for improvement include: enhancing the accuracy in local interaction predictions and increased consideration of the experimental conditions such as multimerization, structure determination method, and time along folding pathways. The prediction of RNA-protein complexes remains the most significant challenge. Finally, given the intrinsic flexibility of many RNAs, we propose the consideration of ensemble models., (© 2023 The Authors. Proteins: Structure, Function, and Bioinformatics published by Wiley Periodicals LLC.)

RNA origami is a method for designing RNA nanostructures that can self-assemble through co-transcriptional folding with applications in nanomedicine and synthetic biology. However, to advance the method further, an improved understanding of RNA structural properties and folding principles is required. Here we use cryogenic electron microscopy to study RNA origami sheets and bundles at sub-nanometre resolution revealing structural parameters of kissing-loop and crossover motifs, which are used to improve designs. In RNA bundle designs, we discover a kinetic folding trap that forms during folding and is only released after 10 h. Exploration of the conformational landscape of several RNA designs reveal the flexibility of helices and structural motifs. Finally, sheets and bundles are combined to construct a multidomain satellite shape, which is characterized by individual-particle cryo-electron tomography to reveal the domain flexibility. Together, the study provides a structural basis for future improvements to the design cycle of genetically encoded RNA nanodevices., (© 2023. The Author(s), under exclusive licence to Springer Nature Limited.)

Objective: Studies have identified perioperative hypothermia as a risk factor for impaired wound healing, increased hospital length of stay, and surgical site infection. This study examines the effect of intraoperative hypothermia on postoperative outcomes in autologous microvascular free flap breast reconstruction., Methods: This was a retrospective review of 55 patients who experienced intraoperative hypothermia, defined as less than 35.0°C core body temperature and 99 normothermic patients who underwent autologous-based microvascular free flap breast reconstruction from 2013 to 2021. Demographics, comorbidities, smoking status, intraoperative warming devices, type of autologous reconstruction, hypothermia (and its duration), and length of surgery were collected. The outcomes assessed were infection rate, reoperation within 90 days, skin necrosis, wound healing complications, hematoma, seroma, and readmission within 90 days., Results: In the study population of 154 consecutive patients, 8.4% had type 1 or type 2 diabetes and 3.2% were current smokers. A total of 90.3% of patients (139) underwent deep inferior epigastric perforator flap reconstruction, 7.1% (11) superficial inferior epigastric artery flap reconstruction, and 4 (2.6%) another free flap type. A total of 35.7% of the patients (55) experienced intraoperative hypothermia defined as less than 35.0°C. In the hypothermic group, a higher proportion of patients had wound healing complications (52.7% vs 29.3%, P < 0.05), hematoma (16.4% vs 5.1%, P < 0.05), and readmission for postoperative complications (34.5% vs 14.1%, P < 0.05). There was also a trend toward higher incidence of seroma (7.3% vs 5.1%), surgical site infection (12.7% vs 9.1%), skin necrosis (12.7% vs 9.1%), and unplanned reoperation within 90 days (10.9% vs 7.1%). Further analysis via Firth logistic regression demonstrated intraoperative hypothermia predicted postoperative hematoma (odds ratio [OR], 3.68; 95% confidence interval [CI], 1.17-11.60; P < 0.05), readmission within 90 days (OR, 3.20; 95% CI, 1.45-7.08; P < 0.05), and wound healing complications (OR, 2.69; 95% CI, 1.36-5.33; P < 0.05)., Conclusions: This study demonstrates that intraoperative hypothermia is a significant risk factor for postoperative wound healing complications, hematoma, and readmission within 90 days in autologous breast reconstruction. Because of a finite amount of donor sites, it is important to find ways to minimize the risk of postoperative complications. Our results support that maintaining strict normothermia during autologous breast reconstruction can significantly improve patient outcomes and reduce morbidity., Competing Interests: Conflicts of interest and sources of funding: none declared., (Copyright © 2023 Wolters Kluwer Health, Inc. All rights reserved.)

Cryogenic electron microscopy (cryo-EM) is a promising method for characterizing the structure of larger RNA structures and complexes. However, the structure of individual aptamers is difficult to solve by cryo-EM due to their low molecular weight and a high signal-to-noise ratio. By placing RNA aptamers on larger RNA scaffolds, the contrast for cryo-EM can be increased to allow the determination of the tertiary structure of the aptamer. Here we use the RNA origami method to scaffold two fluorescent aptamers (Broccoli and Pepper) in close proximity and show that their cognate fluorophores serve as donor and acceptor for FRET. Next, we use cryo-EM to characterize the structure of the RNA origami with the two aptamers to a resolution of 4.4 Å. By characterizing the aptamers with and without ligand, we identify two distinct modes of ligand binding, which are further supported by selective chemical probing. 3D variability analysis of the cryo-EM data show that the relative position between the two bound fluorophores on the origami fluctuate by only 3.5 Å. Our results demonstrate a general approach for using RNA origami scaffolds for characterizing small RNA motifs by cryo-EM and for positioning functional RNA motifs with high spatial precision., (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)

RNA nanotechnology takes advantage of structural modularity to build self-assembling nano-architectures with applications in medicine and synthetic biology. The use of paranemic motifs, that form without unfolding existing secondary structure, allows for the creation of RNA nanostructures that are compatible with cotranscriptional folding in vitro and in vivo. In previous work, kissing-loop (KL) motifs have been widely used to design RNA nanostructures that fold cotranscriptionally. However, the paranemic crossover (PX) motif has not yet been explored for cotranscriptional RNA origami architectures and information about the structural geometry of the motif is unknown. Here, a six base pair-wide paranemic RNA interaction that arranges double helices in a perpendicular manner is introduced, allowing for the generation of a new and versatile building block: the paranemic-crossover triangle (PXT). The PXT is self-assembled by cotranscriptional folding and characterized by cryogenic electron microscopy, revealing for the first time an RNA PX interaction in high structural detail. The PXT is used as a building block for the construction of multimers that form filaments and rings and a duplicated PXT motif is used as a building block to self-assemble cubic structures, demonstrating the PXT as a rigid self-folding domain for the development of wireframe RNA origami architectures., (© 2022 The Authors. Small published by Wiley-VCH GmbH.)

Objectives: The aim of this study was to evaluate the logistics and diagnostic performances of dipstick analyses compared to their counterpart central laboratory analyses for detection of bacteriuria, proteinuria, hyperglycemia, ketosis and hematuria., Design and Methods: Urine dipstick results, urine culture results, flow cytometric cell counts, U-albumin-to-creatinine ratio, P-glucose and P-beta-hydroxybutyrate were retrospectively reviewed in a cohort of consecutive patients admitted to the medical emergency departments of two Danish hospitals. Sensitivity, specificity and predictive values of traditional dipstick analysis were estimated and dipstick was compared to flow cytometry for detection of significant bacteriuria using logistic regression. Turn-around-time for central laboratory analyses were assessed., Results: For each comparison, 1,997 patients or more were included. Traditional dipstick analyses for proteinuria, bacteriuria and ketosis reached sensitivities of up to 90%, while sensitivity for hyperglycemia was 59%. Flow cytometry outperformed traditional dipstick analysis for detection of bacteriuria with a difference in the area under the ROC-curve of 0.07. Turn-around-times for 95% delivery of central laboratory analysis results ranged from approximately 1½ to 2 h., Conclusions: For the detection of bacteriuria and albuminuria, central laboratory analyses reach better performance than dipstick analysis while achieving acceptable turn-around-times and are thus viable alternatives to dipstick analysis. For detection of ketosis and hyperglycemia, dipstick analysis does not perform adequately, but as very short turn-around-time is often required, these conditions may be best diagnosed by point-of-care blood test rather than dipstick or central laboratory analyses. Dipstick hemoglobin analysis, flow cytometry and microscopic evaluation may serve each their distinct purposes, and thus are relevant in the emergency department., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.)

RNA nanotechnology is able to take advantage of the modularity of RNA to build a wide variety of structures and functional devices from a common set of structural modules. The RNA origami architecture harnesses the property of RNA to fold as it is being enzymatically synthesized by the RNA polymerase and enables the design of single-stranded devices that integrate multiple structural and functional RNA motifs. Here, we provide detailed procedures on how to design and characterize RNA origami structures. The process is illustrated by two examples: one that forms lattices and another example that acts as biosensors., (© 2023. Springer Science+Business Media, LLC, part of Springer Nature.)

Background: A myriad of patient education modalities for breast reconstruction exist, although the optimal tools for patient education remain undetermined. The aim of this study is to determine patient preferences for breast reconstruction education modalities based on demographic variables., Methods: A prospective observational study at a tertiary care university health system was conducted between November 2020 and May 2021. A questionnaire was administered to breast reconstruction patients to collect information on demographics, research sources used before the initial appointment, and preferred education modalities. Differences based on age were analyzed using an independent samples t test, whereas a Fisher exact test was used to analyze differences based on ethnicity and education level. Statistical significance was defined as P < .05., Results: The most preferred patient education tools overall were books/written materials and videos. Younger patients were significantly more likely than older patients to have referenced additional physician sources ( P = .0174) and to seek out information on the institution's website ( P = .0465). Those with a college degree were significantly more likely to have performed research prior to the initial appointment ( P = .0206). White patients were significantly more likely than nonwhite patients to talk to friends/family as a research source ( P = .0150)., Conclusions: Regardless of age, education, or ethnicity, most patients prefer books/written materials and video presentations for education on breast reconstruction. Providers should strive to include written and video options to meet the needs of this diverse patient population., (© 2022, HMP Global. All rights reserved. Reproduction in whole or in part prohibited. Content may not be reproduced in any form without written permission. Rights, Permission, Reprint, and Translation information is available at www.hmpglobal.com.)

Designer RNA scaffolds constitute a promising tool for synthetic biology, as they can be genetically expressed to perform specific functions in vivo such as scaffolding enzymatic cascades and regulating gene expression through CRISPR-dCas9 applications. RNA origami is a recently developed RNA design approach that allows construction of large RNA nanostructures that can position aptamer motifs to spatially organize other molecules, including proteins. However, it is still not fully understood how positioning multiple aptamers on a scaffold and the orientation of a scaffold affects functional properties. Here, we investigate fusions of single-guide RNAs and RNA origami scaffolds (termed sgRNAO) capable of recruiting activating domains for control of gene expression in yeast. Using MS2 and PP7 as orthogonal protein-binding aptamers, we observe a gradual increase in transcriptional activation for up to four aptamers. We demonstrate that different aptamer positions on a scaffold and scaffold orientation affect transcriptional activation. Finally, sgRNAOs are used to regulate expression of enzymes of the violacein biosynthesis pathway to control metabolic flux. The integration of RNA origami nanostructures at promoter sites achieved here, can in the future be expanded by the addition of functional motifs such as riboswitches, ribozymes and sensor elements to allow for complex gene regulation., (© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Objective: Plastic surgery education relies heavily on images featuring patient skin tone; while images can be useful representations, it is highly susceptible to implicit bias, a known contributor to healthcare disparities. Using skin tone as a proxy, this study evaluates patient representation in images used in the American Society of Plastic Surgery Resident Education Curriculum., Design: Color photographs, graphics, and videos featured in the American Society of Plastic Surgery "Course Materials" for each module were categorized using the Fitzpatrick scale (I-II, III-IV, or V-VI) by six reviewers. Proportional data and average number ± standard deviation of photos and graphics for each category were reported. Significant difference between Fitzpatrick I to II and V to VI was investigated via a one-way analysis of variance with a Tukey's post-test to adjust for multiple comparisons., Results: An average of 1861 photographs and 237 graphics were assessed with 82% (1518 ± 25.11) of photos and 97% (231 ± 24.45) of graphics categorized as Fitzpatrick I to II. A one-way analysis of variance with a Tukey's post-test demonstrates a statistical difference between images and graphics categorized as Fitzpatrick I to II and Fitzpatrick V to VI (p < 0.001)., Conclusions: Our data reveals an opportunity to improve racial representation in resident education. When 76% of patients in the United States are white and 13% are Black, our findings demonstrate both an unequal and unrepresentative distribution of photos and graphics of non-white patients. Residency is a formative time in a surgeon's career and therefore, exposure to accurate representation of a diverse patient population is of the utmost importance., (Copyright © 2022 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.)

Background: Mastectomy skin flap necrosis (MSFN) can significantly impact outcome after immediate breast reconstruction. Several techniques exist to predict MSFN, but these may require additional testing and information, and they are often not available before surgery. We aim to identify whether breast volume, as calculated from preoperative mammography, can be used as a preoperative predictor of MSFN., Methods: A retrospective chart review from 2010 to 2020 resulted in 378 patients who underwent immediate implant-based breast reconstruction. Complete imaging data were available for 278 patients and 441 reconstructed breasts. Demographic, perioperative, and outcomes data were collected. Measurements from preoperative diagnostic mammograms were used to calculate breast volume. Univariate and multivariate analyses were used to evaluate the association of variables available preoperatively, including breast volume from mammogram and MSFN. Secondary analyses were performed for need for reoperation and loss of reconstruction., Results: On univariate analysis of MSFN development, demographic variables found to be significantly associated with MSFN included body mass index (P = 0.04), diabetes (P = 0.03), and breast volume calculated from routine mammography (P ≤ 0.0001). Average preoperative breast volume via mammography without and with MSFN was 970.6 mL (95% confidence interval [CI], 908.9-1032.3) and 1298.3 mL (95% CI, 1140.0-1456.5) (P < 0.0001), respectively. Statistically significant intraoperative variables for MSFN development included prolonged operative time (P = 0.005), greater initial tissue expander fill volumes (P ≤ 0.001), and prepectoral implant location (P = 0.02). Higher initial tissue expander fill volumes in implant-based reconstructions were associated with increased rates of MSFN, 264.1 mL (95% CI, 247.2-281.0) without MSFN and 349.9 mL (95% CI, 302.0-397.8) in the group with MSFN, respectively (P < 0.001). On multivariate analysis, preoperative imaging volume (P = 0.02) was found to be significant, whereas body mass index and diabetes lost significance (P = 0.40) in association with MSFN., Conclusions: The results of this study establish an association between larger breast volume on preoperative imaging and development of MSFN. This may be useful as a tool for more appropriate patient selection and guidance in the setting of immediate breast reconstruction., Competing Interests: Conflicts of interest and sources of funding: none declared., (Copyright © 2022 Wolters Kluwer Health, Inc. All rights reserved.)

Rational design approaches for the regulation of gene expression are expanding the synthetic biology toolbox. However, only a few tools for regulating gene expression at the translational level have been developed. Here, we devise an approach for translational regulation using the MS2 and PP7 aptamer and coat-protein pairs in Escherichia coli . The aptamers are used as operators in transcription units that encode proteins fused to their cognate coat proteins, which leads to self-repression. RNA origami scaffolds that contain up to four aptamers serve as an alternate binder to activate translation. With this system, we demonstrate that the increase in expression of a reporter protein is dependent on both the concentration and number of aptamers on RNA origami scaffolds. We also demonstrate regulation of multiple proteins using a single MS2 coat protein fusion and apply this method to regulate the relative expression of enzymes of the branched pathway for deoxyviolacein biosynthesis.

Purpose: Hospital-acquired pressure injuries (HAPIs) have significant impacts on patient morbidity and mortality, with approximately 2.5 million patients treated for pressure-related injuries annually.1 This study aimed to describe the influence of a comprehensive wound care team on HAPIs over an 8-year period., Design: Retrospective cohort study., Subjects and Setting: All inpatients at an academic public hospital system with HAPIs during the study period from May 2012 to February 2020., Methods: Data on wound stage, location, infection, medical device location if applicable, and risk factors were recorded from medical records. A 1-way analysis of variance was performed to assess for significance of mean number of cases, National Pressure Injury Advisory Panel (NPIAP) stage on initial presentation, and mean number of medical device-related wounds by year., Results: A total of 957 cases were included. The median stage of pressure injury on assessment was 2, with the mean NPIAP stage declining from 2012 to 2020 (P = .003). Thirty-three percent of pressure injuries were attributed to medical devices, most commonly endotracheal tubing. The most common site of pressure injury was the sacrum (33.6%)., Conclusion: Creation of a comprehensive wound care team within our academic public hospital system demonstrated a significant decline in device-related and pressure injury cases over the past 8 years. The wound care team focused on frequent assessment, education, and evidence-based treatment to lower these HAPI events., (Copyright © 2022 by the Wound, Ostomy and Continence Nurses Society.)

Abstract: Modern breast surgery was first introduced in the United States in 1962 with the use of silicone gel-filled breast implants. Over the past 6 decades, development of breast implants has been challenged by a variety of influencers including aesthetic appeal in shape, texture, and material; challenges in managing outcomes such as contracture, disease, and rupture; and public perception of risks associated with implants. In 1992, silicone breast prostheses were banned by the US Food and Drug Administration with exception for use in breast reconstruction, congenital deformities, or to replace existing implants.The ban led to heightened concerns about implants and possible disease manifestations. Knowledge of the historical evolution of breast prostheses is useful for understanding the associated risks and outcomes unique to each breast implant era. This article aimed to explore characteristics of breast implants by generation, with implications for diagnosis and assistance to modern surgical planning for novice plastic surgeons., Competing Interests: Conflicts of interest and sources of funding: none declared., (Copyright © 2021 Wolters Kluwer Health, Inc. All rights reserved.)

Anticoagulants are commonly utilized during surgeries and to treat thrombotic diseases like stroke and deep vein thrombosis. However, conventional anticoagulants have serious side-effects, narrow therapeutic windows, and lack safe reversal agents (antidotes). Here, an alternative RNA origami displaying RNA aptamers as target-specific anticoagulant is described. Improved design and construction techniques for self-folding, single-molecule RNA origami as a platform for displaying pre-selected RNA aptamers with precise orientational and spatial control are reported. Nuclease resistance is added using 2'-fluoro-modified pyrimidines during in vitro transcription. When four aptamers are displayed on the RNA origami platform, the measured thrombin inhibition and anticoagulation activity is higher than observed for free aptamers, ssRNA-linked RNA aptamers, and RNA origami displaying fewer aptamers. Importantly, thrombin inhibition is immediately switched off by addition of specific reversal agents. Results for single-stranded DNA (ssDNA) and single-stranded peptide nucleic acid (PNA) antidotes show restoration of 63% and 95% coagulation activity, respectively. To demonstrate potential for practical, long-term storage for clinical use, RNA origami is freeze-dried, and stored at room temperature. Freshly produced and freeze-dried RNA show identical levels of activity in coagulation assays. Compared to current commercial intravenous anticoagulants, RNA origami-based molecules show promise as safer alternatives with rapid activity switching for future therapeutic applications., (© 2021 Wiley-VCH GmbH.)

Purpose: Women undergoing postmastectomy breast reconstruction face many complex choices. A myriad of online patient education materials exist to assist in decision making. Understanding of these materials, termed health literacy, affects surgical decision making and outcomes. The National Institutes of Health recommends writing patient education materials at a sixth- to seventh-grade reading level. The primary goal of this study was to assess readability of online breast reconstruction materials., Methods and Materials: Resources were collected from every academic hospital with a plastic surgery residency program, 97 in total. These data were compared with the top nonacademic Web sites ranked by search engine results, 14 in total. Materials were analyzed using 3 validated readability assessment scales: Coleman-Liau Index, SMOG (Simplified Measure of Gobbledygook) Readability Formula, and Flesch-Kincaid Grade Level. Average readability was analyzed, and results were compared using a 1-way analysis of variance to assess for significance between the different tools and a 2-sided t test to assess for significance between academic and nonacademic readability results., Results: The mean readability scores across the academic programs were a Coleman-Liau Index of 13.38 (standard Deviation [SD] 2.81, 13th to 14th grade), Flesch-Kincaid Grade Level of 13.04 (SD = 3.9, 13th grade), and SMOG Readability of 13.64 (SD = 2.99, 13th to 14th grade). For the 14 nonacademic sites, results showed a Coleman-Liau Index of 11.93 (SD = 1.14, 12th grade), Flesch-Kincaid of 11.82 (SD = 2.33, 11th to 12th grade), and SMOG Readability of 10.91 (SD = 1.79, 11th grade). One-way analysis of variance demonstrated no significant differences in mean readability scores across the 3 readability tools used (academic F = 2.7804, P = 0.06; nonacademic F = 1.14, P = 0.33). Two-tailed t test results demonstrated that there was statistical significance between readability of the academic in comparison with nonacademic search engine results (t = 2.04, P = 0.04)., Conclusions: Average readability across all Web sites were much higher than the recommended reading level, at a 13th to 14th grade reading level for academic institutions, and an 11th to 12th grade for nonacademic Web sites. Plastic surgeons may contribute to improving patient understanding and perioperative outcomes through revising patient education materials., Competing Interests: Conflicts of interest and sources of funding: none declared., (Copyright © 2020 Wolters Kluwer Health, Inc. All rights reserved.)

RNA origami is a framework for the modular design of nanoscaffolds that can be folded from a single strand of RNA and used to organize molecular components with nanoscale precision. The design of genetically expressible RNA origami, which must fold cotranscriptionally, requires modelling and design tools that simultaneously consider thermodynamics, the folding pathway, sequence constraints and pseudoknot optimization. Here, we describe RNA Origami Automated Design software (ROAD), which builds origami models from a library of structural modules, identifies potential folding barriers and designs optimized sequences. Using ROAD, we extend the scale and functional diversity of RNA scaffolds, creating 32 designs of up to 2,360 nucleotides, five that scaffold two proteins, and seven that scaffold two small molecules at precise distances. Micrographic and chromatographic comparisons of optimized and non-optimized structures validate that our principles for strand routing and sequence design substantially improve yield. By providing efficient design of RNA origami, ROAD may simplify the construction of custom RNA scaffolds for nanomedicine and synthetic biology.

Background: Dog bite injuries cause significant preventable patient morbidity and health care expenditure in children. This study aimed to characterize the patient and healthcare burden related to pediatric dog bite injuries at a level 1 trauma center., Methods: This is a retrospective review of 356 pediatric patients who presented to Virginia Commonwealth University Pediatric Emergency Department between July 2007 and August 2017 after sustaining dog bite injuries. Demographic information, injury details, management, outcomes, and financial information were analyzed., Results: Most pediatric dog bite injuries afflicted male children (55.6%), ages 6 to 12 years (45.7%), by a household dog (36.2%). The most common offending breed was a pit bull or pit bull mix (53.0%). Infants and grade schoolers were more likely to sustain bites to the head/face (P = 0.001). Usual management consisted of primary repair (75.9%), whereas approximately 25% of the patients required advanced reconstructive techniques. Most patients healed uneventfully, but prolonged antibiotics, additional wound care, or procedures were necessary in 8.4% of the patients. Hospital charges per patient averaged US $8830.70 and tended to be higher in the younger age groups. Insurance status was statistically associated with use of conscious sedation, surgical consult placement, and surgical repair., Conclusions: Although most pediatric dog bite injuries in this study healed uneventfully from primary management in the emergency department, 25% required additional interventions. Furthermore, patient care for these injuries was associated with significant but potentially avoidable personal and financial burden to families. Our data reflect a need for safety education on animal care, behavior, and interaction., Competing Interests: Conflicts of interest and sources of funding: none declared., (Copyright © 2021 Wolters Kluwer Health, Inc. All rights reserved.)

Hospital-acquired burn injuries can result in increased length of hospitalization, costs of stay, and potential for additional procedures. The aim of this study is to describe iatrogenic burn injuries over a 15-year period at an academic public hospital system. Data was collected from January 2004 to June 2019. Data included time of injury, hospital location, mechanism, level of harm caused, and anatomic location of the injury. Demographic information included patient age, gender, body mass index, payer status, primary admission diagnosis and length of stay. 122 patients were identified through an internal hospital database that tracked reported injuries. Incidence was highest between 2005-2012 (12.3 ± 4.1 per year) as compared to 2013-2019 (2.9 ± 2.1 per year). A majority (77%) resulted in harm caused to the patient. Most (41%) of the injuries occurred on the general medical floors, followed by the operating room (33.6%). The most common etiology was scald (23%), followed by electrocautery (14.8%). Five of the injuries resulted in burn consults, although none of these patients required surgery. Iatrogenic burns appear to be decreasing. While a majority were reported to have caused patient harm, none were serious enough to warrant surgery. Most injuries occurred on the medical floors with a scald mechanism. This review presents an opportunity to emphasize in-hospital burn prevention, as well as an opportunity for the burn team to affect change in concert with hospital administration., (© The Author(s) 2021. Published by Oxford University Press on behalf of the American Burn Association. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Background: Bleeding is associated with a significantly increased morbidity and mortality. Bleeding events are often described in the unstructured text of electronic health records, which makes them difficult to identify by manual inspection., Objectives: To develop a deep learning model that detects and visualizes bleeding events in electronic health records., Patients/methods: Three hundred electronic health records with International Classification of Diseases, Tenth Revision diagnosis codes for bleeding or leukemia were extracted. Each sentence in the electronic health record was annotated as positive or negative for bleeding. The annotated sentences were used to develop a deep learning model that detects bleeding at sentence and note level., Results: On a balanced test set of 1178   sentences, the best-performing deep learning model achieved a sensitivity of 0.90, specificity of 0.90, and negative predictive value of 0.90. On a test set consisting of 700 notes, of which 49 were positive for bleeding, the model achieved a note-level sensitivity of 1.00, specificity of 0.52, and negative predictive value of 1.00. By using a sentence-level model on a note level, the model can explain its predictions by visualizing the exact sentence in a note that contains information regarding bleeding. Moreover, we found that the model performed consistently well across different types of bleedings., Conclusions: A deep learning model can be used to detect and visualize bleeding events in the free text of electronic health records. The deep learning model can thus facilitate systematic assessment of bleeding risk, and thereby optimize patient care and safety., (© 2021 The Authors. Research and Practice in Thrombosis and Haemostasis published by Wiley Periodicals LLC on behalf of International Society on Thrombosis and Haemostasis (ISTH).)

To further understand the transcriptome, new tools capable of measuring folding, interactions, and localization of RNA are needed. Although Förster resonance energy transfer (FRET) is an angle- and distance-dependent phenomenon, the majority of FRET measurements have been used to report distances, by assuming rotationally averaged donor-acceptor pairs. Angle-dependent FRET measurements have proven challenging for nucleic acids due to the difficulties in incorporating fluorophores rigidly into local substructures in a biocompatible manner. Fluorescence turn-on RNA aptamers are genetically encodable tags that appear to rigidly confine their cognate fluorophores, and thus have the potential to report angular-resolved FRET. Here, we use the fluorescent aptamers Broccoli and Mango-III as donor and acceptor, respectively, to measure the angular dependence of FRET. Joining the two fluorescent aptamers by a helix of variable length allowed systematic rotation of the acceptor fluorophore relative to the donor. FRET oscillated in a sinusoidal manner as a function of helix length, consistent with simulated data generated from models of oriented fluorophores separated by an inflexible helix. Analysis of the orientation dependence of FRET allowed us to demonstrate structural rigidification of the NiCo riboswitch upon transition metal-ion binding. This application of fluorescence turn-on aptamers opens the way to improved structural interpretation of ensemble and single-molecule FRET measurements of RNA., (© 2021 Jeng et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.)

Objectives: Pneumatic tube transportation of samples is an effective way of reducing turn-around-time, but evidence of the effect of pneumatic tube transportation on urine samples is lacking. We thus wished to investigate the effect of pneumatic tube transportation on various components in urine, in order to determine if pneumatic tube transportation of these samples is feasible., Methods: One-hundred fresh urine samples were collected in outpatient clinics and partitioned with one partition being carried by courier to the laboratory, while the other was sent by pneumatic tube system (Tempus600). Both partitions were then analysed for soluble components and particles, and the resulting mean difference and limits of agreement were calculated., Results: Albumin, urea nitrogen, creatinine, protein and squamous epithelial cells were unaffected by transportation in the Tempus600 system, while bacteria, renal tubular epithelial cells, white blood cells and red blood cells were affected and potassium and sodium may have been affected., Conclusions: Though pneumatic tube transportation did affect some of the investigated components, in most cases the changes induced were clinically acceptable, and hence samples could be safely transported by the Tempus600 pneumatic tube system. For bacteria, white blood cells and red blood cells local quality demands will determine if pneumatic tube transportation is appropriate., (© 2020 Walter de Gruyter GmbH, Berlin/Boston.)

Acute and adaptive changes in systemic markers of oxidatively generated nucleic acid modifications (i.e., 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) and 8-oxo-7,8-dihydroguanosine (8-oxoGuo)) as well as inflammatory cytokines (i.e., C-reactive protein, interleukin-6, interleukin-10, and tumour necrosis factor alpha), a liver hormone (i.e., fibroblast growth factor 21 (FGF21)), and bone metabolism markers (sclerostin, osteocalcin, C-terminal telopeptide, and N-terminal propeptide of type 1 procollagen) were investigated following a marathon in 20 study participants. Immediate changes were observed in inflammatory cytokines, FGF21, and bone metabolism markers following the marathon. In contrast, no immediate changes in urinary excretion of 8-oxodG and 8-oxoGuo were evident. Four days after the marathon, decreased urinary excretion of 8-oxodG (-2.9 (95% CI -4.8;-1.1) nmol/24 h, P  < 0.01) and 8-oxoGuo (-5.8 (95% CI -10.3;-1.3) nmol/24 h, P  = 0.02) was observed. The excretion rate of 8-oxodG remained decreased 7 days after the marathon compared to baseline (-2.3 (95%CI -4.3;-0.4) nmol/24 h, P  = 0.02), whereas the excretion rate of 8-oxoGuo was normalized. In conclusion marathon participation immediately induced a considerable inflammatory response, but did not increase excretion rates of oxidatively generated nucleic acid modifications. In fact, a delayed decrease in oxidatively generated nucleic acid modifications was observed suggesting adaptive antioxidative effects following exercise., Abbreviations: 8-oxodG: 8-oxo-7,8-dihydro-2'-deoxyguanosine; 8-oxoGuo: 8-oxo-7,8-dihydroguanosine; CI: confidence interval; CTX: C-terminal telopeptide of type 1 collagen; DXA: dual-energy X-ray absorptiometry; ELISA: enzyme-linked immunosorbent assay; FGF21: Fibroblast growth factor 21; h: hour; hsCRP: high sensitivity C-reactive protein; IL: interleukin; IQR: interquartile range; MS: mass spectrometry: P1NP: N-terminal propeptide of type 1 procollagen; TNFα: tumour necrosis factor alpha; UPLC: ultra-performance liquid chromatography.

In biological systems, large and complex structures are often assembled from multiple simpler identical subunits. This strategy-homooligomerization-allows efficient genetic encoding of structures and avoids the need to control the stoichiometry of multiple distinct units. It also allows the minimal number of distinct subunits when designing artificial nucleic acid structures. Here, we present a robust self-assembly system in which homooligomerizable tiles are formed from intramolecularly folded RNA single strands. Tiles are linked through an artificially designed branched kissing-loop motif, involving Watson-Crick base pairing between the single-stranded regions of a bulged helix and a hairpin loop. By adjusting the tile geometry to gain control over the curvature, torsion and the number of helices, we have constructed 16 different linear and circular structures, including a finite-sized three-dimensional cage. We further demonstrate cotranscriptional self-assembly of tiles based on branched kissing loops, and show that tiles inserted into a transfer RNA scaffold can be overexpressed in bacterial cells.

Objective: Increasing the amounts of functionally competent brown adipose tissue (BAT) in adult humans has the potential to restore dysfunctional metabolism and counteract obesity. In this study, we aimed to characterize the human perirenal fat depot, and we hypothesized that there would be regional, within-depot differences in the adipose signature depending on local sympathetic activity., Methods: We characterized fat specimens from four different perirenal regions of adult kidney donors, through a combination of qPCR mapping, immunohistochemical staining, RNA-sequencing, and pre-adipocyte isolation. Candidate gene signatures, separated by adipocyte morphology, were recapitulated in a murine model of unilocular brown fat induced by thermoneutrality and high fat diet., Results: We identified widespread amounts of dormant brown adipose tissue throughout the perirenal depot, which was contrasted by multilocular BAT, primarily found near the adrenal gland. Dormant BAT was characterized by a unilocular morphology and a distinct gene expression profile, which partly overlapped with that of subcutaneous white adipose tissue (WAT). Brown fat precursor cells, which differentiated into functional brown adipocytes were present in the entire perirenal fat depot, regardless of state. We identified SPARC as a candidate adipokine contributing to a dormant BAT state, and CLSTN3 as a novel marker for multilocular BAT., Conclusions: We propose that perirenal adipose tissue in adult humans consists mainly of dormant BAT and provide a data set for future research on factors which can reactivate dormant BAT into active BAT, a potential strategy for combatting obesity and metabolic disease., (Copyright © 2019 The Authors. Published by Elsevier GmbH.. All rights reserved.)

Nucleic acid aptamers selected for thrombin binding have been previously shown to possess anticoagulant activity; however, problems with rapid renal clearance and short circulation half-life have prevented translation to clinical usefulness. Here, a family of self-folding, functional RNA origami molecules bearing multiple thrombin-binding RNA aptamers and showing significantly improved anticoagulant activity is described. These constructs may overcome earlier problems preventing clinical use of nucleic acid anticoagulants. RNA origami structures are designed in silico and produced by in vitro transcription from DNA templates. Incorporation of 2'-fluoro-modified C- and U-nucleotides is shown to increase nuclease resistance and stability during long-term storage. Specific binding to human thrombin as well as high stability in the presence of RNase A and in human plasma, comparatively more stable than DNA is demonstrated. The RNA origami constructs show anticoagulant activity sevenfold greater than free aptamer and higher than previous DNA weave tiles decorated with DNA aptamers. Anticoagulation activity is maintained after at least 3 months of storage in buffer at 4 °C. Additionally, inhibition of thrombin is shown to be reversed by addition of single-stranded DNA antidotes. This project paves the way for development of RNA origami for potential therapeutic applications especially as a safer surgical anticoagulant., (© 2019 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)