-
Computational and Structural... 2022RNA-binding proteins are central players in post-transcriptional regulation. Some of them, such as the well-studied bacterial RNA chaperones Hfq and ProQ or the...
RNA-binding proteins are central players in post-transcriptional regulation. Some of them, such as the well-studied bacterial RNA chaperones Hfq and ProQ or the eukaryotic RNAi factor Argonaute, interact with hundreds-to-thousands of different RNAs and thereby globally affect gene expression. As a shared yet limited resource, these and other RNA-binding hubs drive strong competition between their multiple ligands. This creates a ground for significant cross-communication between RNA targets, which enables them to share information, "synchronise" their behaviour, and produce interesting biochemical effects, sometimes propagating across the highly connected RNA-protein network. This property is likely universally present in hub-centred networks and plays a key role in global gene expression programmes. It is also an important factor in biotechnology and synthetic biology applications of RNA/protein-based circuits. However, few studies so-far focused on describing and explaining this phenomenon from first principles. Here we introduce an information theory-based framework to comprehensively and exactly describe information flow in hub-centred networks. We show that information sharing can achieve significant levels in relatively small networks, provided the hub is present in limiting concentrations. The transmitted information is sufficient to noticeably affect the binding probabilities of competing targets but drops exponentially along the network. Target overexpression can disrupt communication between other targets, while hub sequestration boosts the crosstalk. We also find that overlaps between the interactomes of two different hubs create both entropic challenges and new forms of long-range communication between RNAs and proteins.
PubMed: 36420147
DOI: 10.1016/j.csbj.2022.11.019 -
Radiology Apr 2023
Topics: Female; Humans; Ultrasonography; Adnexal Diseases; Neoplasms; Magnetic Resonance Imaging
PubMed: 36413134
DOI: 10.1148/radiol.222866 -
Clinical Orthopaedics and Related... Feb 2023Classic (static) Roentgen stereophotogrammetric analysis (RSA) is the current gold standard to assess, in vivo, the migration of total joint arthroplasty components. To...
BACKGROUND
Classic (static) Roentgen stereophotogrammetric analysis (RSA) is the current gold standard to assess, in vivo, the migration of total joint arthroplasty components. To prevent potential patient motion artifacts during the acquisition of paired radiostereometric images, images must be taken by simultaneously firing both X-ray tubes. However, the influence of nonsynchronized RSA paired images or patient motion artifacts on the precision of RSA and the assessment of implant migration is not well understood.
QUESTIONS/PURPOSES
We assessed (1) the effect of possible patient motion on the precision of RSA and (2) apparent differences in implant migration among axes (in-plane and out-of-plane translations and in-plane and out-of-plane rotations) of possible motion artifacts.
METHODS
Radiographs of two tibial knee arthroplasty components, each fixed in two bone-implant models as a customized phantom, were taken in a uniplanar measurement setup. We evaluated both model-based (implant models from reversed engineering) and marker-based (additional attached implant markers) RSA approaches. Between the simulated reference and follow-up examinations, we used one of the bone-implant models to simulate patient motion and the other to simulate no patient motion in parallel. Two defined protocols were followed for each of the bone-implant models: no-motion and simulated motion protocols. RSA image pairs were analyzed using a model-based RSA software package (MBRSA 4.1, RSA core ). Precision was calculated through repeat examinations, and migration of the two components was assessed for comparison of the components with each other. Measurements were taken along the medial-lateral and posterior-anterior axes for translations and around the cranial-caudal axis for rotations. The maximum total point motion was measured for comparison between the two components.
RESULTS
The effect of simulated patient motion was generally small, except in the cranial-caudal axis, but the induced imprecision associated with motion was larger in model-based RSA than it was in marker-based RSA. The mean ± standard deviation values of precision in model-based RSA were 0.035 ± 0.015 mm, 0.045 ± 0.014 mm, and 0.049 ± 0.036 mm greater than those in marker-based RSA, in accordance with the simulated motion protocol in translations along the medial-lateral axis (0.018 ± 0.004 mm; p = 0.01), along the posterior-anterior axis (0.018 ± 0.007 mm; p = 0.003), and rotations around the cranial-caudal axis (0.017 ± 0.006 mm; p = 0.02). Apparent differences in implant migration were the greatest for the maximum total point motion. The maximum total point motion increased from 0.038 ± 0.007 mm for the no-motion protocol to 1.684 ± 0.038 mm (p < 0.001) for the simulated motion protocol in marker-based RSA, and from 0.101 ± 0.027 mm for the no-motion protocol to 1.973 ± 0.442 mm (p < 0.001) for the simulated motion protocol in model-based RSA, and was the worst-case scenario regarding patient motion artifacts.
CONCLUSION
Patient motion exceeding 1 mm or 1° on nonsynchronized RSA images affects measurement errors regarding the detection of migration of a tibial component. In clinical RSA studies, the effect of patient motion on the assessment of implant migration should be of particular concern, even if clinical RSA systems have acceptable precision. Specially trained radiographers are crucial for correctly acquiring radiographs, especially when simultaneous radiography exposures are not electronically automated. In general, RSA requires synchronized image acquisition, and this should be the state-of-the-art.
CLINICAL RELEVANCE
In clinical RSA studies, precision assessed by repeat examinations may not be reliable using the current standards that are widely used in radiology departments. When assessing implant migration for reliability, comparison of the maximum total point motion between the tested (simulated motion) implant and baseline (no-motion) implant, as in this study, is advocated because of the accurate detection of patient motion artifacts.
Topics: Humans; Arthroplasty, Replacement, Knee; Reproducibility of Results; Artifacts; Radiostereometric Analysis; Tibia
PubMed: 36398327
DOI: 10.1097/CORR.0000000000002453 -
BioRxiv : the Preprint Server For... Nov 2022Eukaryotic cell-free protein synthesis (CFPS) systems have the potential to simplify and speed up the expression and high-throughput analysis of complex proteins with...
Eukaryotic cell-free protein synthesis (CFPS) systems have the potential to simplify and speed up the expression and high-throughput analysis of complex proteins with functionally relevant post-translational modifications (PTMs). However, low yields and the inability to scale such systems have so far prevented their widespread adoption in protein research and manufacturing. Here, we present a detailed demonstration for the capabilities of a CFPS system derived from BY-2 cell culture (BY-2 lysate; BYL). BYL is able to express diverse, functional proteins at high yields in under 48 hours, complete with native disulfide bonds and N-glycosylation. An optimised version of the technology is commercialised as 'ALiCE ', engineered for high yields of up to 3 mg/mL. Recent advances in the scaling of BYL production methodologies have allowed scaling of the CFPS reaction. We show simple, linear scale-up of batch mode reporter proten expression from a 100 μL microtiter plate format to 10 mL and 100 mL volumes in standard Erlenmeyer flasks, culminating in preliminary data from 1 L reactions in a CELL-tainer® CT20 rocking motion bioreactor. As such, these works represent the first published example of a eukaryotic CFPS reaction scaled past the 10 mL level by several orders of magnitude. We show the ability of BYL to produce the simple reporter protein eYFP and large, multimeric virus-like particles directly in the cytosolic fraction. Complex proteins are processed using the native microsomes of BYL and functional expression of multiple classes of complex, difficult-to-express proteins is demonstrated, specifically: a dimeric, glycoprotein enzyme, glucose oxidase; the monoclonal antibody adalimumab; the SARS-Cov-2 receptor-binding domain; human epidermal growth factor; and a G protein-coupled receptor membrane protein, cannabinoid receptor type 2. Functional binding and activity are shown using a combination of surface plasmon resonance techniques, a serology-based ELISA method and a G protein activation assay. Finally, in-depth post-translational modification (PTM) characterisation of purified proteins through disulfide bond and N-glycan analysis is also revealed - previously difficult in the eukaryotic CFPS space due to limitations in reaction volumes and yields. Taken together, BYL provides a real opportunity for screening of complex proteins at the microscale with subsequent amplification to manufacturing-ready levels using off-the-shelf protocols. This end-to-end platform suggests the potential to significantly reduce cost and the time-to-market for high value proteins and biologics.
PubMed: 36380753
DOI: 10.1101/2022.11.10.515920 -
Journal of Digital Imaging Feb 2023Building a document-level classifier for COVID-19 on radiology reports could help assist providers in their daily clinical routine, as well as create large numbers of...
Building a document-level classifier for COVID-19 on radiology reports could help assist providers in their daily clinical routine, as well as create large numbers of labels for computer vision models. We have developed such a classifier by fine-tuning a BERT-like model initialized from RadBERT, its continuous pre-training on radiology reports that can be used on all radiology-related tasks. RadBERT outperforms all biomedical pre-trainings on this COVID-19 task (P<0.01) and helps our fine-tuned model achieve an 88.9 macro-averaged F1-score, when evaluated on both X-ray and CT reports. To build this model, we rely on a multi-institutional dataset re-sampled and enriched with concurrent lung diseases, helping the model to resist to distribution shifts. In addition, we explore a variety of fine-tuning and hyperparameter optimization techniques that accelerate fine-tuning convergence, stabilize performance, and improve accuracy, especially when data or computational resources are limited. Finally, we provide a set of visualization tools and explainability methods to better understand the performance of the model, and support its practical use in the clinical setting. Our approach offers a ready-to-use COVID-19 classifier and can be applied similarly to other radiology report classification tasks.
Topics: Humans; COVID-19; Radiology; Research Report; Natural Language Processing
PubMed: 36323915
DOI: 10.1007/s10278-022-00714-8 -
BMJ (Clinical Research Ed.) Oct 2022To assess the comparative effectiveness of computed tomography and invasive coronary angiography in women and men with stable chest pain suspected to be caused by... (Randomized Controlled Trial)
Randomized Controlled Trial
Comparative effectiveness of initial computed tomography and invasive coronary angiography in women and men with stable chest pain and suspected coronary artery disease: multicentre randomised trial.
OBJECTIVE
To assess the comparative effectiveness of computed tomography and invasive coronary angiography in women and men with stable chest pain suspected to be caused by coronary artery disease.
DESIGN
Prospective, multicentre, randomised pragmatic trial.
SETTING
Hospitals at 26 sites in 16 European countries.
PARTICIPANTS
2002 (56.2%) women and 1559 (43.8%) men (total of 3561 patients) with suspected coronary artery disease referred for invasive coronary angiography on the basis of stable chest pain and a pre-test probability of obstructive coronary artery disease of 10-60%.
INTERVENTION
Both women and men were randomised 1:1 (with stratification by gender and centre) to a strategy of either computed tomography or invasive coronary angiography as the initial diagnostic test (1019 and 983 women, and 789 and 770 men, respectively), and an intention-to-treat analysis was performed. Randomised allocation could not be blinded, but outcomes were assessed by investigators blinded to randomisation group.
MAIN OUTCOME MEASURES
The primary endpoint was major adverse cardiovascular events (MACE; cardiovascular death, non-fatal myocardial infarction, or non-fatal stroke). Key secondary endpoints were an expanded MACE composite (cardiovascular death, non-fatal myocardial infarction, non-fatal stroke, transient ischaemic attack, or major procedure related complication) and major procedure related complications.
RESULTS
Follow-up at a median of 3.5 years was available in 98.9% (1979/2002) of women and in 99.0% (1544/1559) of men. No statistically significant gender interaction was found for MACE (P=0.29), the expanded MACE composite (P=0.45), or major procedure related complications (P=0.11). In both genders, the rate of MACE did not differ between the computed tomography and invasive coronary angiography groups. In men, the expanded MACE composite endpoint occurred less frequently in the computed tomography group than in the invasive coronary angiography group (22 (2.8%) 41 (5.3%); hazard ratio 0.52, 95% confidence interval 0.31 to 0.87). In women, the risk of having a major procedure related complication was lower in the computed tomography group than in the invasive coronary angiography group (3 (0.3%) 21 (2.1%); hazard ratio 0.14, 0.04 to 0.46).
CONCLUSION
This study found no evidence for a difference between women and men in the benefit of using computed tomography rather than invasive coronary angiography as the initial diagnostic test for the management of stable chest pain in patients with an intermediate pre-test probability of coronary artery disease. An initial computed tomography scan was associated with fewer major procedure related complications in women and a lower frequency of the expanded MACE composite in men.
TRIAL REGISTRATION
NCT02400229ClinicalTrials.gov NCT02400229.
Topics: Female; Humans; Male; Coronary Angiography; Coronary Artery Disease; Prospective Studies; Chest Pain; Tomography, X-Ray Computed; Myocardial Infarction; Stroke; Computed Tomography Angiography; Predictive Value of Tests
PubMed: 36261169
DOI: 10.1136/bmj-2022-071133 -
Translational Lung Cancer Research Sep 2022Lung cancer screening may provide a favorable opportunity for a spirometry examination, to diagnose participants with undiagnosed lung function impairments, or to...
Lung function impairment in the German Lung Cancer Screening Intervention Study (LUSI): prevalence, symptoms, and associations with lung cancer risk, tumor histology and all-cause mortality.
BACKGROUND
Lung cancer screening may provide a favorable opportunity for a spirometry examination, to diagnose participants with undiagnosed lung function impairments, or to improve targeting of computed tomography (CT) screening intensity in view of expected net benefit.
METHODS
Spirometry was performed in the CT screening arm (n=2,029) of the German Lung Cancer Screening Intervention Study (LUSI)-a trial examining the effects of annual CT screening on lung cancer mortality, in 50-69-year-old long-term smokers. Participants were classified as having chronic obstructive pulmonary disease (COPD) [forced expiration in one second (FEV)/forced vital lung capacity (FVC) <0.7], preserved ratio impaired spirometry (PRISm; FEV/FVC ≥0.7 and FEV% predicted <80%), or normal spirometry. Descriptive statistics were used to examine associations of COPD or PRISm with respiratory symptoms, and self-reported medical diagnoses of respiratory and other morbidities. Logistic regression and proportional hazards regression were used to examine associations of COPD and PRISm, as well as their self-reported medical diagnoses, with risks of lung cancer and all-cause mortality.
RESULTS
A total of 1,987 screening arm participants (98%) provided interpretable spirometry measurements; of these, 34.3% had spirometric patterns consistent with either COPD (18.6%) or PRISm (15.7%). Two thirds of participants with COPD or PRISm were asymptomatic, and only 23% reported a previous medical diagnosis concordant with COPD. Participants reporting a diagnosis tended to be more often current and heavier smokers, and more often had respiratory symptoms, cardiovascular comorbidities, or more severe lung function impairments. Independently of smoking history, moderate-to-severe (GOLD 2-4) COPD (OR =2.14; 95% CI: 1.54-2.98), and PRISm (OR =2.68; 95% CI: 1.61-4.40), were associated with increased lung cancer risk. Lung cancer patients with PRISm less frequently had adenocarcinomas, and more often squamous cell or small cell tumors, compared to those with normal spirometry (n=45), and both PRISm and COPD were associated with more advanced lung cancer tumor stage for screen-detected cancers. PRISm and COPD, depending on GOLD stage, were also associated with about 2- to 4-fold increases in risk of overall mortality, which to 87 percent had causes other than lung cancer.
CONCLUSIONS
About one third of smokers eligible for lung cancer screening in Germany have COPD or PRISm. As these conditions were associated with detection of lung cancer, spirometry may help identify populations at high risk for death of lung cancer or other causes, and who might particularly benefit from CT screening.
PubMed: 36248328
DOI: 10.21037/tlcr-22-63 -
Scientific Reports Oct 2022Cementless calcar-guided femoral short stems in total hip arthroplasty (THA) have become increasingly popular over the years. Early distal migration of femoral stems...
Cementless calcar-guided femoral short stems in total hip arthroplasty (THA) have become increasingly popular over the years. Early distal migration of femoral stems measured by Einzel-Bild-Roentgen Analyse, Femoral Component Analyse (EBRA-FCA) has been reported to be a risk factor for aseptic loosening. The aim of this study was to analyse axial migration behavior and subsidence of a new short stem (launched in 2015) over a follow-up period of 3 years. According to the study protocol, 100 hip osteoarthritis patients who consecutively received an unilateral cementless calcar-guided short stem (ANA.NOVA proxy) at a single department were prospectively included in this mid-term follow-up study. Thirteen patients were lost to follow-up, resulting in 87 patients with unilateral THA who fulfilled the criteria for migration analysis with EBRA-FCA. The cohort comprised 41 males (mean age: 60 ± 16.5; mean BMI (Body Mass Index): 30 ± 13) and 46 females (mean age: 61 ± 15.5; mean BMI: 27 ± 10). Seven standardized radiographs per patient were analyzed with EBRA-FCA. An average migration of 2.0 mm (0.95-3.35) was observed within the first 3 years. The median increase during the first year was higher than in the second and third year (1.2 mm [IQR: 0.5-2.15] vs. 0.3 mm [IQR: 0.1-0.6 mm] vs. 0.25 mm [IQR: 0.1-0.5 mm]. Detected migration did not lead to stem loosening, instability, dislocation, or revision surgery in any patient. A higher risk for subsidence was observed in male and heavyweight patients, whereas the female gender was associated with a lower risk. No correlation between migration and revision could be observed. Although moderate subsidence was detectable, the performance of the short stem ANA.NOVA proxy is encouraging. Yet, its use may be re-considered in overweight and male patients due to more pronounced subsidence.
Topics: Adult; Aged; Arthroplasty, Replacement, Hip; Female; Femur; Follow-Up Studies; Hip Prosthesis; Humans; Male; Middle Aged; Osteoarthritis, Hip; Prosthesis Design; Retrospective Studies
PubMed: 36229640
DOI: 10.1038/s41598-022-22160-w -
Radiology. Imaging Cancer Sep 2022
Topics: Female; Humans; Magnetic Resonance Imaging; Ovarian Cysts; Thyroid Nodule
PubMed: 36178353
DOI: 10.1148/rycan.220121 -
The Plant Journal : For Cell and... Oct 2022The spatial organization of protein synthesis in the eukaryotic cell is essential for maintaining the integrity of the proteome and the functioning of the cell....
The spatial organization of protein synthesis in the eukaryotic cell is essential for maintaining the integrity of the proteome and the functioning of the cell. Translation on free polysomes or on ribosomes associated with the endoplasmic reticulum has been studied for a long time. More recent data have revealed selective translation of mRNAs in other compartments, in particular at the surface of mitochondria. Although these processes have been described in many organisms, particularky in plants, the mRNA targeting and localized translation mechanisms remain poorly understood. Here, the Arabidopsis thaliana Friendly (FMT) protein is shown to be a cytosolic RNA binding protein that associates with cytosolic ribosomes at the surface of mitochondria. FMT knockout delays seedling development and causes mitochondrial clustering. The mutation also disrupts the mitochondrial proteome, as well as the localization of nuclear transcripts encoding mitochondrial proteins at the surface of mitochondria. These data indicate that FMT participates in the localization of mRNAs and their translation at the surface of mitochondria.
Topics: Proteome; Ribosomes; Mitochondria; Mitochondrial Proteins; RNA-Binding Proteins; RNA, Messenger; Arabidopsis; Protein Biosynthesis
PubMed: 36050837
DOI: 10.1111/tpj.15962