Mining raw plant transcriptomic data for new cyclopeptide alkaloids.

In recent years, genome and transcriptome mining have dramatically expanded the rate of discovering diverse natural products from bacteria and fungi. In plants, this approach is often more limited due to the lack of available annotated genomes and transcriptomes combined with a less consistent clustering of biosynthetic genes. The recently identified burpitide class of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products offer a valuable opportunity for bioinformatics-guided discovery in plants due to their short biosynthetic pathways and gene encoded substrates. Using a high-throughput approach to assemble and analyze 700 publicly available raw transcriptomic data sets, we uncover the potential distribution of split burpitide precursor peptides in Streptophyta. Metabolomic analysis of target plants confirms our bioinformatic predictions of new cyclopeptide alkaloids from both known and new sources.

Patient experience of the process to diagnosis of chronic limb-threatening ischaemia: A qualitative study.

INTRODUCTION: Delays exist at each stage of the chronic limb-threatening ischaemia (CLTI) care pathway, but there is little known about patient factors influencing delay to diagnosis of CLTI. This study explores the experiences and perceptions of patients recently diagnosed with CLTI. METHODS: A qualitative interview study was conducted. Sixteen participants underwent semi-structured interviews. Reflexive thematic analysis was performed on the data, aiming to understand factors which can influence delay in the CLTI care pathway. RESULTS: Five interrelated themes were developed: CLTI is a devastating condition; Reluctance to ask for help; When we are empowered we get better care; Luck plays a role in the process to diagnosis; and Vascular units can do better, comprising sub-themes of information transfer-consider communication and arterial versus non-arterial centres-proximity isn't everything. CONCLUSIONS: The five themes generated from the interview data describe factors relevant to delay given meaning by participants who have lived experience of CLTI. Theme content should be noted by clinicians, commissioners and providers looking to improve care pathways for patients with CLTI. The importance of awareness for the public, patients and clinicians linked ideas in some themes and interventions to raise awareness should be considered.

High-resolution magic angle spinning nuclear magnetic resonance of donor pancreatic tissue may predict islet viability prior to isolation.

For patients with type 1 diabetes mellitus complicated by severe hypoglycemia, clinical islet transplantation is an efficacious alternative to whole pancreas transplantation. While islet transplantation has improved over the last few years, there remain questions regarding its cost-effectiveness and donor allosensitization, which is exacerbated when islets from more than one donor are required. Understanding the features of a pancreas that would provide viable islets prior to isolation may lead to development of an accurate assay that could identify suitable pancreases and provide significant cost savings to a clinical islet transplantation program. In this pilot study, solid-state high-resolution magic angle spinning (HRMAS) nuclear magnetic resonance (NMR) spectroscopy was used to assess samples of convenience of human pancreatic tissue taken prior to islet isolation both before and after incubation using the two-layer perfluorocarbon (PFC)/University of Wisconsin (UW) solution cold-storage method. We observed that, prior to incubation, human pancreatic tissue exhibited evidence of hypoxia with decreased peak integrals associated with glucose and increased peak integrals corresponding to lactate and free fatty acids. After incubation, we observed a reversal of the hypoxia-induced damage, as integrals corresponding to glucose increased, and those corresponding to lactate and free fatty acid resonances decreased. Interestingly, a significant correlation between the ratio of the glucose integral (at 3.0-4.5 ppm) to the sum of the fatty acid (at 0.9 ppm) and lactate + fatty acid (at 1.3 ppm) integrals and glucose responsiveness, a measure of islet viability, of the isolated islets, was observed after incubation in PFC/UW solution for pancreases that responded to PFC/UW solution incubation (p = 0.02). Notably, pancreases with little or no change in the integral ratio after PFC/UW solution incubation had poor recovery. These results suggest that tissue recovery is a key feature for determining islet cell viability, and further that HRMAS NMR may be a practical method to quickly assess human donor pancreatic tissue prior to islet isolation for clinical transplantation.

Temporal Trends in End-Tidal Capnography and Outcomes in Out-of-Hospital Cardiac Arrest: A Secondary Analysis of a Randomized Clinical Trial.

Importance: While widely measured, the time-varying association between exhaled end-tidal carbon dioxide (EtCO2) and out-of-hospital cardiac arrest (OHCA) outcomes is unclear. Objective: To evaluate temporal associations between EtCO2 and return of spontaneous circulation (ROSC) in the Pragmatic Airway Resuscitation Trial (PART). Design, Setting, and Participants: This study was a secondary analysis of a cluster randomized trial performed at multicenter emergency medical services agencies from the Resuscitation Outcomes Consortium. PART enrolled 3004 adults (aged ≥18 years) with nontraumatic OHCA from December 1, 2015, to November 4, 2017. EtCO2 was available in 1172 cases for this analysis performed in June 2023. Interventions: PART evaluated the effect of laryngeal tube vs endotracheal intubation on 72-hour survival. Emergency medical services agencies collected continuous EtCO2 recordings using standard monitors, and this secondary analysis identified maximal EtCO2 values per ventilation and determined mean EtCO2 in 1-minute epochs using previously validated automated signal processing. All advanced airway cases with greater than 50% interpretable EtCO2 signal were included, and the slope of EtCO2 change over resuscitation was calculated. Main Outcomes and Measures: The primary outcome was ROSC determined by prehospital or emergency department palpable pulses. EtCO2 values were compared at discrete time points using Mann-Whitney test, and temporal trends in EtCO2 were compared using Cochran-Armitage test of trend. Multivariable logistic regression was performed, adjusting for Utstein criteria and EtCO2 slope. Results: Among 1113 patients included in the study, 694 (62.4%) were male; 285 (25.6%) were Black or African American, 592 (53.2%) were White, and 236 (21.2%) were another race; and the median (IQR) age was 64 (52-75) years. Cardiac arrest was most commonly unwitnessed (n = 579 [52.0%]), nonshockable (n = 941 [84.6%]), and nonpublic (n = 999 [89.8%]). There were 198 patients (17.8%) with ROSC and 915 (82.2%) without ROSC. Median EtCO2 values between ROSC and non-ROSC cases were significantly different at 10 minutes (39.8 [IQR, 27.1-56.4] mm Hg vs 26.1 [IQR, 14.9-39.0] mm Hg; P < .001) and 5 minutes (43.0 [IQR, 28.1-55.8] mm Hg vs 25.0 [IQR, 13.3-37.4] mm Hg; P < .001) prior to end of resuscitation. In ROSC cases, median EtCO2 increased from 30.5 (IQR, 22.4-54.2) mm HG to 43.0 (IQR, 28.1-55.8) mm Hg (P for trend < .001). In non-ROSC cases, EtCO2 declined from 30.8 (IQR, 18.2-43.8) mm Hg to 22.5 (IQR, 12.8-35.4) mm Hg (P for trend < .001). Using adjusted multivariable logistic regression with slope of EtCO2, the temporal change in EtCO2 was associated with ROSC (odds ratio, 1.45 [95% CI, 1.31-1.61]). Conclusions and Relevance: In this secondary analysis of the PART trial, temporal increases in EtCO2 were associated with increased odds of ROSC. These results suggest value in leveraging continuous waveform capnography during OHCA resuscitation. Trial Registration: ClinicalTrials.gov Identifier: NCT02419573.

Control of cyanobacterial growth with potassium; implications for bloom control in nuclear storage ponds.

Microbial blooms have been reported in the First Generation Magnox Storage Pond at the Sellafield Nuclear Facility. The pond is kept alkaline with NaOH to minimise fuel rod corrosion, however alkali-tolerant microbial blooms dominated by the cyanobacterium Pseudanabaena catenata are able to thrive in this hostile environment. This study assessed the impact of alternative alkali-dosing regimens (KOH versus NaOH treatment) on biomass accumulation, using a P. catenata dominated mixed culture, which is representative of the pond environment. Optical density was reduced by 40-67 % with KOH treatment over the 3-month chemostat experiment. Microbial community analysis and proteomics demonstrated that the KOH-dependent inhibition of cell growth was mostly specific to P. catenata. The addition of KOH to nuclear storage ponds may therefore help control growth of this pioneer photosynthetic organism due to its sensitivity to potassium, while maintaining the high pH needed to inhibit the corrosion of stored nuclear fuel.

Triple Aspiration Versus Conventional Aspiration Techniques: A Randomized In-Vitro Evaluation.

BACKGROUND AND PURPOSE: A single aspiration maneuver using a large volume syringe is a common and effective technique for aspiration thrombectomy. Multiple aspiration cycles using large aspiration syringes has been proposed as a means to improve efficacy over single aspiration. In this study, we sought to investigate the efficacy of a "triple aspiration technique" where a large volume syringe is cycled three times prior to catheter retraction during aspiration thrombectomy. MATERIALS AND METHODS: A 3D-printed adult vasculature was used as a benchtop thrombectomy platform. Fibrin-rich and red blood cell-rich clots were prepared in centrifuge tubes using human plasma, red blood cells, and calcium chloride. Next, clots were placed in the carotid terminus of the model, and the performances of three different aspiration techniques-triple syringe, single syringe, and continuous pump aspiration-were compared in a randomized manner (1:1:1). Outcomes of interest included first-pass efficacy (FPE), complete clot removal (final mTICI 2c/3), the number of thrombectomy attempts to achieve mTICI 2c/3, vacuum pressure, and distal embolization. The distal emboli were detected using a 70-micron cell strainer placed at the outflow of the model and quantified using an image processing algorithm. The vacuum pressures were measured using a pressure transducer (Honeywell, NC, USA). RESULTS: A total of 102 replicates were performed, 34 for each technique. The triple aspiration technique provided a significantly higher rate of FPE than the syringe and pump aspiration techniques (67.6% vs. 41.1%, p= 0.02). Additionally, the triple aspiration technique achieved complete clot removal with a significantly lower number of thrombectomy attempts compared to single syringe aspiration (1.2 ± 0.5 vs. 1.8 ± 0.8, p=0.005). The triple aspiration technique generated significantly higher vacuum pressure than both the single syringe and vacuum pump aspiration (28.3 ± 0.2 vs. 27.2 ± 0.3 (p= 0.002) and 26.2 ± 0.4 (p=0.001), respectively). The differences in complete clot removal and distal embolization parameters were not statistically significantly different across the groups. CONCLUSIONS: Our findings suggest that the triple aspiration technique can improve FPE rates and vacuum pressure in aspiration thrombectomy. Further studies are needed to examine the safety and efficacy of triple aspiration in the clinical setting. ABBREVIATIONS: AcommA = anterior communicating artery; FPE = first pass efficacy; ICA = internal carotid artery; MCA = middle cerebral artery; MT = mechanical thrombectomy; mTICI = modified thrombolysis in cerebral infarction scale; PcommA = posterior communicating artery.

Body MRI in pediatrics: where we are and what the future holds.

Body magnetic resonance imaging (MRI) is increasingly used for disease diagnosis, characterization, and monitoring in children of all ages. MRI has numerous advantages when compared to other imaging modalities, including a lack of ionizing radiation, superior soft tissue image contrast, and ability to provide objective, quantitative assessments. As MRI continues to evolve, pediatric body MRI examinations of the future will certainly be different than our current and past protocols. In this review article, we will discuss the present and likely future states of pediatric body MRI, including the increasing application of quantitative MRI methods, faster imaging techniques and implementation of abbreviated targeted protocols, and the growing use of artificial intelligence methods.

Illness Trajectories After Revascularization in Patients With Peripheral Artery Disease: A Unified Approach to Understanding the Risk of Major Amputation and Death.

BACKGROUND: The aim of this study was to investigate the illness trajectories of patients with peripheral artery disease (PAD) after revascularization and estimate the independent risks of major amputation and death (from any cause) and their interaction. METHODS: Data from Hospital Episode Statistics Admitted Patient Care were used to identify patients (≥50 years of age) who underwent lower limb revascularization for PAD in England from April 2013 to March 2020. A Markov illness-death model was developed to describe patterns of survival after the initial lower limb revascularization, if and when patients experienced major amputation, and survival after amputation. The model was also used to investigate the association between patient characteristics and these illness trajectories. We also analyzed the relative contribution of deaths after amputation to overall mortality and how the risk of mortality after amputation was related to the time from the index revascularization to amputation. RESULTS: The study analyzed 94 690 patients undergoing lower limb revascularization for PAD from 2013 to 2020. The majority were men (65.6%), and the median age was 72 years (interquartile range, 64-79). One-third (34.8%) of patients had nonelective revascularization, whereas others had elective procedures. For nonelective patients, the amputation rate was 15.2% (95% CI, 14.4-16.0) and 19.9% (19.0-20.8) at 1 and 5 years after revascularization, respectively. For elective patients, the corresponding amputation rate was 2.7% (95% CI, 2.4-3.1) and 5.3% (4.9-5.8). Overall, the risk of major amputation was higher among patients who were younger, had tissue loss, diabetes, greater frailty, nonelective revascularization, and more distal procedures. The mortality rate at 5 years after revascularization was 64.3% (95% CI, 63.2-65.5) for nonelective patients and 33.0% (32.0-34.1) for elective patients. After major amputation, patients were at an increased risk of mortality if they underwent major amputation within 6 months after the index revascularization. CONCLUSIONS: The illness-death model provides an integrated framework to understand patient outcomes after lower limb revascularization for PAD. Although mortality increased with age, the study highlights patients <60 years of age were at increased risk of major amputation, particularly after nonelective revascularization.

Rapid abdominopelvic MR imaging in the emergency department: establishing a program and addressing the challenges.

Utilization of magnetic resonance imaging (MRI) in the pediatric emergency room or urgent care setting for abdominopelvic indications has been increasing. The creation and implementation of rapid urgent MRI programs can have various challenges. The purpose of this article is to describe a framework for the creation of a rapid urgent abdominopelvic MRI program in the pediatric emergency room setting.

Increasing acceptance of AI-generated digital twins through clinical trial applications.

Today's approach to medicine requires extensive trial and error to determine the proper treatment path for each patient. While many fields have benefited from technological breakthroughs in computer science, such as artificial intelligence (AI), the task of developing effective treatments is actually getting slower and more costly. With the increased availability of rich historical datasets from previous clinical trials and real-world data sources, one can leverage AI models to create holistic forecasts of future health outcomes for an individual patient in the form of an AI-generated digital twin. This could support the rapid evaluation of intervention strategies in silico and could eventually be implemented in clinical practice to make personalized medicine a reality. In this work, we focus on uses for AI-generated digital twins of clinical trial participants and contend that the regulatory outlook for this technology within drug development makes it an ideal setting for the safe application of AI-generated digital twins in healthcare. With continued research and growing regulatory acceptance, this path will serve to increase trust in this technology and provide momentum for the widespread adoption of AI-generated digital twins in clinical practice.

Single Cell Transcriptome Analysis During Development in Dictyostelium.

Dictyostelium represents a stripped-down model for understanding how cells make decisions during development. The complete life cycle takes around a day and the fully differentiated structure is composed of only two major cell types. With this apparent reduction in "complexity," single cell transcriptomics has proven to be a valuable tool in defining the features of developmental transitions and cell fate separation events, even providing causal information on how mechanisms of gene expression can feed into cell decision-making. These scientific outputs have been strongly facilitated by the ease of non-disruptive single cell isolation-allowing access to more physiological measures of transcript levels. In addition, the limited number of cell states during development allows the use of more straightforward analysis tools for handling the ensuing large datasets, which provides enhanced confidence in inferences made from the data. In this chapter, we will outline the approaches we have used for handling Dictyostelium single cell transcriptomic data, illustrating how these approaches have contributed to our understanding of cell decision-making during development.

This year sees an opportunity for long-needed oral health reforms. Cancer patients, in particular, stand to benefit.

The long-standing divide in Australia between medicine and dentistry has left many with inequitable access to dental care. People with oral cancer, in particular, may have few options for dental rehabilitation after cancer treatment, even with private health insurance. However, 2024 could finally see health care reforms that address these inequities, with significant momentum building in Australia. In this Perspective, we argue for a national approach to reforms that incorporate aspects of preventive health, primary health care, Medicare Benefits Schedule item review, and the value of Private Health Insurance rebates for dental care.

Lipid-associated macrophages reshape BAT cell identity in obesity.

Obesity and type 2 diabetes cause a loss in brown adipose tissue (BAT) activity, but the molecular mechanisms that drive BAT cell remodeling remain largely unexplored. Using a multilayered approach, we comprehensively mapped a reorganization in BAT cells. We uncovered a subset of macrophages as lipid-associated macrophages (LAMs), which were massively increased in genetic and dietary model of BAT expansion. LAMs participate in this scenario by capturing extracellular vesicles carrying damaged lipids and mitochondria released from metabolically stressed brown adipocytes. CD36 scavenger receptor drove LAM phenotype, and CD36-deficient LAMs were able to increase brown fat genes in adipocytes. LAMs released transforming growth factor ß1 (TGF-ß1), which promoted the loss of brown adipocyte identity through aldehyde dehydrogenase 1 family member A1 (Aldh1a1) induction. These findings unfold cell dynamic changes in BAT during obesity and identify LAMs as key responders to tissue metabolic stress and drivers of loss of brown adipocyte identity.

Mutant Nrf2E79Q enhances the promotion and progression of a subset of oncogenic Ras keratinocytes and skin tumors.

Squamous cell carcinomas (SCCs), including lung, head & neck, bladder, and skin SCCs often display constitutive activation of the KEAP1-NRF2 pathway. Constitutive activation is achieved through multiple mechanisms, including activating mutations in NFE2L2 (NRF2). To determine the functional consequences of Nrf2 activation on skin SCC development, we assessed the effects of mutant Nrf2E79Q expression, one of the most common activating mutations in human SCCs, on tumor promotion and progression in the mouse skin multistage carcinogenesis model using a DMBA-initiation/TPA-promotion protocol where the Hras A->T mutation (Q61L) is the canonical driver mutation. Nrf2E79Q expression was temporally and conditionally activated in the epidermis at two stages of tumor development: 1) after DMBA initiation in the epidermis but before cutaneous tumor development and 2) in pre-existing DMBA-initiated/TPA-promoted squamous papillomas. Expression of Nrf2E79Q in the epidermis after DMBA initiation but before tumor occurrence inhibited the development/promotion of 70% of squamous papillomas. However, the remaining papillomas often displayed non-canonical Hras and Kras mutations and enhanced progression to SCCs compared to control mice expressing wildtype Nrf2. Nrf2E79Q expression in pre-existing tumors caused rapid regression of 60% of papillomas. The remaining papillomas displayed the expected canonical Hras A->T mutation (Q61L) and enhanced progression to SCCs. These results demonstrate that mutant Nrf2E79Q enhances the promotion and progression of a subset of skin tumors and alters the frequency and diversity of oncogenic Ras mutations when expressed early after initiation.

Evaluation of 3D T1-weighted spoiled gradient echo MR image quality using artificial intelligence image reconstruction techniques in the pediatric brain.

PURPOSE: To assess image quality and diagnostic confidence of 3D T1-weighted spoiled gradient echo (SPGR) MRI using artificial intelligence (AI) reconstruction. MATERIALS AND METHODS: This prospective, IRB-approved study enrolled 50 pediatric patients (mean age = 11.8 ± 3.1 years) undergoing clinical brain MRI. In addition to standard of care (SOC) compressed SENSE (CS = 2.5), 3D T1-weighted SPGR images were obtained with higher CS acceleration factors (5 and 8) to evaluate the ability of AI reconstruction to improve image quality and reduce scan time. Images were reviewed independently on dedicated research PACS workstations by two neuroradiologists. Quantitative analysis of signal intensities to calculate apparent grey and white matter signal to noise (aSNR) and grey-white matter apparent contrast to noise ratios (aCNR) was performed. RESULTS: AI improved overall image quality compared to standard CS reconstruction in 35% (35/100) of evaluations in CS = 2.5 (average scan time = 221 ± 6.9 s), 100% (46/46) of CS = 5 (average scan time = 113.3 ± 4.6 s) and 94% (47/50) of CS = 8 (average scan time = 74.1 ± 0.01 s). Quantitative analysis revealed significantly higher grey matter aSNR, white matter aSNR and grey-white matter aCNR with AI reconstruction compared to standard reconstruction for CS 5 and 8 (all p-values < 0.001), however not for CS 2.5. CONCLUSIONS: AI reconstruction improved overall image quality and gray-white matter qualitative and quantitative aSNR and aCNR in highly accelerated (CS = 5 and 8) 3D T1W SPGR images in the majority of pediatric patients.

Compositionally unique mitochondria in filopodia support cellular migration.

Local metabolic demand within cells varies widely and the extent to which individual mitochondria can be specialized to meet these functional needs is unclear. We examined the subcellular distribution of MICOS, a spatial and functional organizer of mitochondria, and discovered that it dynamically enriches at the tip of a minor population of mitochondria in the cell periphery that we term "METEORs". METEORs have a unique composition; MICOS enrichment sites are depleted of mtDNA and matrix proteins and contain high levels of the Ca2+ uniporter MCU, suggesting a functional specialization. METEORs are also enriched for the myosin MYO19, which promotes their trafficking to a small subset of filopodia. We identify a positive correlation between the length of filopodia and the presence of METEORs and show that elimination of mitochondria from filopodia impairs cellular motility. Our data reveal a novel type of mitochondrial heterogeneity and suggest compositionally specialized mitochondria support cell migration.