ABSTRACT
This study explores the application of the RIP3-caspase3-assay in heterogeneous spheroid cultures to analyze cell death pathways, emphasizing the nuanced roles of apoptosis and necroptosis. By employing directly conjugated monoclonal antibodies, we provide detailed insights into the complex mechanisms of cell death. Our findings demonstrate the assay's capability to differentiate between RIP1-independent apoptosis, necroptosis, and RIP1-dependent apoptosis, marking a significant advancement in organoid research. Additionally, we investigate the effects of TNFα on isolated intestinal epithelial cells, revealing a concentration-dependent response and an adaptive or threshold reaction to TNFα-induced stress. The results indicate a preference for RIP1-independent cell death pathways upon TNFα stimulation, with a notable increase in apoptosis and a secondary role of necroptosis. Our research underscores the importance of the RIP3-caspase3-assay in understanding cell death mechanisms in organoid cultures, offering valuable insights for disease modeling and the development of targeted therapies. The assay's adaptability and robustness in spheroid cultures enhances its potential as a tool in personalized medicine and translational research.
Subject(s)
Apoptosis , Caspase 3 , Necroptosis , Receptor-Interacting Protein Serine-Threonine Kinases , Spheroids, Cellular , Receptor-Interacting Protein Serine-Threonine Kinases/metabolism , Humans , Spheroids, Cellular/metabolism , Spheroids, Cellular/drug effects , Caspase 3/metabolism , Apoptosis/drug effects , Necroptosis/drug effects , Tumor Necrosis Factor-alpha/metabolism , Tumor Necrosis Factor-alpha/pharmacology , Cell Death/drug effects , Organoids/metabolism , Organoids/cytologyABSTRACT
The excitation of acoustic waves by a unidirectional transducer, integrated in a piezoelectric cylindrical tube or disk, can lead to a time-independent torque. This phenomenon, demonstrated earlier in experiments and analyzed with coupling-of mode theory, is explained in detail, starting on the level of lattice dynamics of a piezoelectric crystal. Expressions are derived for the stationary torque in the form of integrals over the volume or surface of the piezoelectric, involving the electric potential and displacement field associated with the acoustic waves generated by the transducer. Simulations have been carried out with the help of the finite element method for a tube made of PZT for two cases: A pre-defined potential on the surface of the tube and metal electrodes buried in the piezoelectric. The displacement field and electric potential of the high-frequency acoustic waves (between 200 and 300 kHz) were computed and used in the evaluation of the integrals. The attenuation due to various loss channels of the acoustic waves in the system has been analyzed in detail, as this plays a crucial role for the efficiency of torque generation. It is conjectured that time-reversal symmetry, present in the absence of attenuation, prohibits the generation of a static torque at least in the linear limit. A qualitative comparison is made between the simulations and earlier experiments. Discrepancies are attributed to lack of knowledge of the relevant material constants of the piezoelectric and to a simplified modeling of the electrode geometry in the cylindrical tube, which was necessary for reasons of numerical accuracy.
ABSTRACT
Background: Acute liver injury is a life-threatening condition with disparate aetiology. Swift and adequate interdisciplinary treatment is essential to assure the best possible outcomes in these patients. Investigations to identify the cause of the condition and the implementation of quick and appropriate treatment can be lifesaving. Case Presentation. In October 2022, an otherwise healthy 66-year-old male presented at the University Hospital Essen with acute liver injury following an inclisiran injection for hypercholesterinaemia. Four weeks following admission, the patient fully recovered after initially receiving short-term cortisol therapy and open albumin (OPAL) dialysis, and the indices of liver, kidney, and coagulation function were normal at discharge. Conclusion: This is to our knowledge the first reported acute liver injury due to an inclisiran injection. Cortisol in combination with OPAL dialysis is an effective method for the treatment of acute liver injury caused by inclisiran injury, and in this case, it led to a near-complete reversal of the acute liver injury at the time of discharge.
ABSTRACT
Homeostatic control of intracellular ionic strength is essential for protein, organelle and genome function, yet mechanisms that sense and enable adaptation to ionic stress remain poorly understood in animals. We find that the transcription factor NFAT5 directly senses solution ionic strength using a C-terminal intrinsically disordered region. Both in intact cells and in a purified system, NFAT5 forms dynamic, reversible biomolecular condensates in response to increasing ionic strength. This self-associative property, conserved from insects to mammals, allows NFAT5 to accumulate in the nucleus and activate genes that restore cellular ion content. Mutations that reduce condensation or those that promote aggregation both reduce NFAT5 activity, highlighting the importance of optimally tuned associative interactions. Remarkably, human NFAT5 alone is sufficient to reconstitute a mammalian transcriptional response to ionic or hypertonic stress in yeast. Thus NFAT5 is both the sensor and effector of a cell-autonomous ionic stress response pathway in animal cells.
ABSTRACT
We have studied the stability of the smallest long-lived all carbon molecular dianion (C_{7}^{2-}) in new time domains and with a single ion at a time using a cryogenic electrostatic ion-beam storage ring. We observe spontaneous electron emission from internally excited dianions on millisecond timescales and monitor the survival of single colder C_{7}^{2-} molecules on much longer timescales. We find that their intrinsic lifetime exceeds several minutes-6 orders of magnitude longer than established from earlier experiments on C_{7}^{2-}. This is consistent with our calculations of vertical electron detachment energies predicting one inherently stable isomer and one isomer which is stable or effectively stable behind a large Coulomb barrier for C_{7}^{2-}âC_{7}^{-}+e^{-} separation.
ABSTRACT
PURPOSE/OBJECTIVE: Deep-inspiration breath-hold (DIBH) during radiotherapy may reduce dose to the lungs and heart compared to treatment in free breathing. However, intra-fractional target shifts between several breath-holds may decrease target coverage. We compared target shifts between four DIBHs at the planning-CT session with those measured on CBCT-scans obtained pre- and post-DIBH treatments. MATERIAL/METHODS: Twenty-nine lung cancer and nine lymphoma patients were treated in DIBH. An external gating block was used as surrogate for the DIBH-level with a window of 2 mm. Four DIBH CT-scans were acquired: one for planning (CTDIBH3) and three additional (CTDIBH1,2,4) to assess the intra-DIBH target shifts at scanning by registration to CTDIBH3. During treatment, pre-treatment (CBCTpre) and post-treatment (CBCTpost) scans were acquired. For each pair of CBCTpre/post, the target intra-DIBH shift was determined. For lung cancer, tumour (GTV-Tlung) and lymph nodes (GTV-Nlung) were analysed separately. Group mean (GM), systematic and random errors, and GM for the absolute maximum shifts (GMmax) were calculated for the shifts between CTDIBH1,2,3,4 and between CBCTpre/post. RESULTS: For GTV-Tlung, GMmax was larger at CBCT than CT in all directions. GMmax in cranio-caudal direction was 3.3 mm (CT)and 6.1 mm (CBCT). The standard deviations of the shifts in the left-right and cranio-caudal directions were larger at CBCT than CT. For GTV-Nlung and CTVlymphoma, no difference was found in GMmax or SD. CONCLUSION: Intra-DIBH shifts at planning-CT session are generally smaller than intra-DIBH shifts observed at CBCTpre/post and therefore underestimate the intra-fractional DIBH uncertainty during treatment. Lung tumours show larger intra-fractional variations than lymph nodes and lymphoma targets.
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More effective treatments for fentanyl use disorder are urgently needed. An emerging literature indicates that glucagon-like peptide-1 receptor (GLP-1R) agonists attenuate voluntary opioid taking and seeking in rodents. However, GLP-1R agonists produce adverse malaise-like effects that may limit patient compliance. Recently, we developed a dual agonist of GLP-1Rs and neuropeptide Y2 receptors (Y2Rs) that attenuates fentanyl taking and seeking at doses that do not produce malaise-like effects in opioid-experienced rats. Whether activating Y2Rs alone is sufficient to reduce opioid taking and seeking, however, is not known. Here, we investigated the efficacy of the Y2R ligand PYY3-36 to reduce fentanyl self-administration and the reinstatement of fentanyl-seeking behavior, a model of relapse in humans. Male rats were allowed to self-administer fentanyl (2.5 µg/kg, i.v.) for 21 days on a fixed-ratio 5 (FR5) schedule of reinforcement. Rats were then pretreated with vehicle or PYY3-36 (50 µg/kg s.c.; 0.1 and 1.0 µg/100 nL intra-VTA) prior to fentanyl self-administration test sessions. There were no effects of systemic or intra-VTA PYY3-36 on intravenous fentanyl self-administration. Opioid taking was then extinguished. Prior to subsequent reinstatement test sessions, rats were pretreated with vehicle or PYY3-36 (50 µg/kg s.c.; 0.1 and 1.0 µg/100 nL intra-VTA). Both systemic and intra-VTA administration of PYY3-36 attenuated fentanyl reinstatement in male rats at doses that did not affect food intake or produce adverse malaise-like effects. These findings indicate that Y2R agonism alone is sufficient to decrease fentanyl-seeking behavior during abstinence in opioid-experienced rats and further support strategies aimed at targeting Y2Rs for treating opioid use disorders.
Subject(s)
Fentanyl , Opioid-Related Disorders , Humans , Rats , Male , Animals , Fentanyl/pharmacology , Rats, Sprague-Dawley , Analgesics, Opioid , Reinforcement, Psychology , Self AdministrationABSTRACT
PURPOSE: Patients with BRAFV600E-mutant metastatic colorectal cancer (mCRC) have a dismal prognosis. The best strategies in these patients remain elusive. Against this background, we report the clinical course of patients with BRAFV600E-mutant mCRC to retrieve the best treatment strategy. PATIENTS AND METHODS: Clinico-pathological data were extracted from the electronic health records. Kaplan-Meier method was used to estimate overall (OS) and progression-free survival (PFS). Objective response rate (ORR) was assessed according to RECIST 1.1. RESULTS: In total, 51 patients were enrolled. FOLFOXIRI was administered to 12 patients; 29 patients received FOLFOX or FOLFIRI as first-line treatment. Median OS was 17.6 months. Median PFS with FOLFOXIRI (13.0 months) was significantly prolonged (HR 0.325) as compared to FOLFOX/FOLFIRI (4.3 months). However, this failed to translate into an OS benefit (p = 0.433). Interestingly, addition of a monoclonal antibody to chemotherapy associated with superior OS (HR 0.523). A total of 64.7% patients received further-line therapy, which included a BRAF inhibitor in 17 patients. Targeted therapy associated with very favourable OS (25.1 months). CONCLUSION: Patients with BRAFV600E-mutated mCRC benefit from the addition of an antibody to first-line chemotherapy. Further-line treatment including a BRAF inhibitor has a dramatic impact on survival.
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RATIONALE: Nicotine cessation is associated with increased consumption of highly palatable foods and body weight gain in most smokers. Concerns about body weight gain are a major barrier to maintaining long-term smoking abstinence, and current treatments for nicotine use disorder (NUD) delay, but do not prevent, body weight gain during abstinence. Glucagon-like peptide-1 receptor (GLP-1R) agonists reduce food intake and are FDA-approved for treating obesity. However, the effects of GLP-1R agonist monotherapy on nicotine seeking and withdrawal-induced hyperphagia are unknown. OBJECTIVES: We screened the efficacy of the long-lasting GLP-1R agonist liraglutide to reduce nicotine-mediated behaviors including voluntary nicotine taking, as well as nicotine seeking and hyperphagia during withdrawal. METHODS: Male and female rats self-administered intravenous nicotine (0.03 mg/kg/inf) for ~21 days. Daily liraglutide administration (25 µg/kg, i.p.) started on the last self-administration day and continued throughout the extinction and reinstatement phases of the experiment. Once nicotine taking was extinguished, the reinstatement of nicotine-seeking behavior was assessed after an acute priming injection of nicotine (0.2 mg/kg, s.c.) and re-exposure to conditioned light cues. Using a novel model of nicotine withdrawal-induced hyperphagia, intake of a high fat diet (HFD) was measured during home cage abstinence in male and female rats with a history of nicotine self-administration. RESULTS: Liraglutide attenuated nicotine self-administration and reinstatement in male and female rats. Repeated liraglutide attenuated withdrawal-induced hyperphagia and body weight gain in male and female rats at a dose that was not associated with malaise-like effects. CONCLUSIONS: These findings support further studies investigating the translational potential of GLP-1R agonists to treat NUD.
Subject(s)
Nicotine , Tobacco Use Disorder , Female , Rats , Male , Animals , Liraglutide/pharmacology , Tobacco Use Disorder/drug therapy , Obesity/drug therapy , Hyperphagia/drug therapy , Hyperphagia/prevention & control , Self Administration , Extinction, PsychologicalABSTRACT
BACKGROUND: Pancreatic cancer has a dismal prognosis. One reason is resistance to cytotoxic drugs. Molecularly matched therapies might overcome this resistance but the best approach to identify those patients who may benefit is unknown. Therefore, we sought to evaluate a molecularly guided treatment approach. MATERIALS AND METHODS: We retrospectively analyzed the clinical outcome and mutational status of patients with pancreatic cancer who received molecular profiling at the West German Cancer Center Essen from 2016 to 2021. We carried out a 47-gene DNA next-generation sequencing (NGS) panel. Furthermore, we assessed microsatellite instability-high/deficient mismatch repair (MSI-H/dMMR) status and, sequentially and only in case of KRAS wild-type, gene fusions via RNA-based NGS. Patient data and treatment were retrieved from the electronic medical records. RESULTS: Of 190 included patients, 171 had pancreatic ductal adenocarcinoma (90%). One hundred and three patients had stage IV pancreatic cancer at diagnosis (54%). MMR analysis in 94 patients (94/190, 49.5%) identified 3 patients with dMMR (3/94, 3.2%). Notably, we identified 32 patients with KRAS wild-type status (16.8%). To identify driver alterations in these patients, we conducted an RNA-based fusion assay on 13 assessable samples and identified 5 potentially actionable fusions (5/13, 38.5%). Overall, we identified 34 patients with potentially actionable alterations (34/190, 17.9%). Of these 34 patients, 10 patients (10/34, 29.4%) finally received at least one molecularly targeted treatment and 4 patients had an exceptional response (>9 months on treatment). CONCLUSIONS: Here, we show that a small-sized gene panel can suffice to identify relevant therapeutic options for pancreatic cancer patients. Informally comparing with previous large-scale studies, this approach yields a similar detection rate of actionable targets. We propose molecular sequencing of pancreatic cancer as standard of care to identify KRAS wild-type and rare molecular subsets for targeted treatment strategies.
Subject(s)
Pancreatic Neoplasms , Proto-Oncogene Proteins p21(ras) , Humans , Retrospective Studies , Proto-Oncogene Proteins p21(ras)/genetics , Pancreatic Neoplasms/drug therapy , Pancreatic Neoplasms/genetics , Genomics , Pancreatic NeoplasmsABSTRACT
Positively charged repeat peptides are emerging as key players in neurodegenerative diseases. These peptides can perturb diverse cellular pathways but a unifying framework for how such promiscuous toxicity arises has remained elusive. We used mass-spectrometry-based proteomics to define the protein targets of these neurotoxic peptides and found that they all share similar sequence features that drive their aberrant condensation with these positively charged peptides. We trained a machine learning algorithm to detect such sequence features and unexpectedly discovered that this mode of toxicity is not limited to human repeat expansion disorders but has evolved countless times across the tree of life in the form of cationic antimicrobial and venom peptides. We demonstrate that an excess in positive charge is necessary and sufficient for this killer activity, which we name 'polycation poisoning'. These findings reveal an ancient and conserved mechanism and inform ways to leverage its design rules for new generations of bioactive peptides.
ABSTRACT
BACKGROUND: Patient-reported physical function (PF) is a key endpoint in cancer clinical trials. Using complex statistical methods, common metrics have been developed to compare scores from different patient-reported outcome (PRO) measures, but such methods do not account for possible differences in questionnaire content. Therefore, the aim of our study was a content comparison of frequently used PRO measures for PF in cancer patients. METHODS: Relying on the framework of the International Classification of Functioning, Disability and Health (ICF) we categorized the item content of the physical domains of the following measures: EORTC CAT Core, EORTC QLQ-C30, SF-36, PROMIS Cancer Item Bank for Physical Function, PROMIS Short Form for Physical Function 20a, and the FACT-G. Item content was linked to ICF categories by two independent reviewers. RESULTS: The 118 items investigated were assigned to 3 components ('d - Activities and Participation', 'b - Body Functions', and 'e - Environmental Factors') and 11 first-level ICF categories. All PF items of the EORTC measures but one were assigned to the first-level ICF categories 'd4 - Mobility' and 'd5 - Self-care', all within the component 'd - Activities and Participation'. The SF-36 additionally included item content related to 'd9 - Community, social and civic life' and the PROMIS Short Form for Physical Function 20a also included content related to 'd6 - domestic life'. The PROMIS Cancer Item Bank (v1.1) covered, in addition, two first-level categories within the component 'b - Body Functions'. The FACT-G Physical Well-being scale was found to be the most diverse scale with item content partly not covered by the ICF framework. DISCUSSION: Our results provide information about conceptual differences between common PRO measures for the assessment of PF in cancer patients. Our results complement quantitative information on psychometric characteristics of these measures and provide a better understanding of the possibilities of establishing common metrics.
Subject(s)
Disabled Persons , Neoplasms , Humans , International Classification of Functioning, Disability and Health , Patient Reported Outcome Measures , Surveys and Questionnaires , Neoplasms/therapy , Disability Evaluation , Activities of Daily Living , Quality of LifeABSTRACT
BACKGROUND: Receiving a diagnosis of multiple sclerosis (MS) can be stressful; later, patients may conceal their diagnosis. Here, we aimed to (1) assess prevalence of disclosure and concealment behaviors, and (2) explore whether diagnosis experience is associated with later concealment and if MS provider engagement on this topic modifies concealment. METHODS: In a survey-based study, MS patients completed DISCO-MS assessing disclosure and concealment and responded to questions about diagnosis experience and practitioner attention to disclosure. Frequency analysis and Pearson's correlations were used in exploratory analyses. RESULTS: 428 adults with MS participated. 49% (N = 201) conceal their diagnosis. Higher education [t(405) = 3.66, p < 0.001], younger age (r = -0.15, p = 0.002), and shorter disease duration (r = -0.18, p = 0.010) were associated with higher concealment. 39% (N = 159) anticipate negative consequences of disclosure. Individuals reporting positive diagnosis experience (26%, N = 102) were less likely to conceal later in disease course compared to those with negative experience (34%, N = 136) [t(233) = 2.483, p = 0.014]. Patients whose MS providers discussed disclosure (23%, N = 73) anticipated less negative consequences of disclosure [t(323) = 2.475, p = 0.014]. CONCLUSIONS: Diagnosis concealment is common in MS. Favorable diagnosis experience and provider attention to the topic of disclosure throughout the MS disease course may influence diagnosis concealment.
Subject(s)
Multiple Sclerosis , Adult , Humans , Multiple Sclerosis/diagnosis , Multiple Sclerosis/epidemiology , Surveys and QuestionnairesABSTRACT
Platinum (Pt) compounds such as oxaliplatin are among the most commonly prescribed anti-cancer drugs. Despite their considerable clinical impact, the molecular basis of platinum cytotoxicity and cancer specificity remain unclear. Here we show that oxaliplatin, a backbone for the treatment of colorectal cancer, causes liquid-liquid demixing of nucleoli at clinically relevant concentrations. Our data suggest that this biophysical defect leads to cell-cycle arrest, shutdown of Pol I-mediated transcription, and ultimately cell death. We propose that instead of targeting a single molecule, oxaliplatin preferentially partitions into nucleoli, where it modifies nucleolar RNA and proteins. This mechanism provides a general approach for drugging the increasing number of cellular processes linked to biomolecular condensates.
Subject(s)
Antineoplastic Agents , Platinum , Oxaliplatin/pharmacology , Platinum/metabolism , Cell Nucleolus/metabolism , Antineoplastic Agents/pharmacology , Antineoplastic Agents/metabolism , RNA Polymerase I/metabolismABSTRACT
A hallmark pathological feature of the neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) is the depletion of RNA-binding protein TDP-43 from the nucleus of neurons in the brain and spinal cord1. A major function of TDP-43 is as a repressor of cryptic exon inclusion during RNA splicing2-4. Single nucleotide polymorphisms in UNC13A are among the strongest hits associated with FTD and ALS in human genome-wide association studies5,6, but how those variants increase risk for disease is unknown. Here we show that TDP-43 represses a cryptic exon-splicing event in UNC13A. Loss of TDP-43 from the nucleus in human brain, neuronal cell lines and motor neurons derived from induced pluripotent stem cells resulted in the inclusion of a cryptic exon in UNC13A mRNA and reduced UNC13A protein expression. The top variants associated with FTD or ALS risk in humans are located in the intron harbouring the cryptic exon, and we show that they increase UNC13A cryptic exon splicing in the face of TDP-43 dysfunction. Together, our data provide a direct functional link between one of the strongest genetic risk factors for FTD and ALS (UNC13A genetic variants), and loss of TDP-43 function.
Subject(s)
Amyotrophic Lateral Sclerosis , Frontotemporal Dementia , Amyotrophic Lateral Sclerosis/metabolism , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Exons/genetics , Frontotemporal Dementia/metabolism , Genome-Wide Association Study , Humans , Motor Neurons/pathology , Nerve Tissue ProteinsABSTRACT
OBJECTIVES: There is limited knowledge regarding the specific interrelationships between urgent coronary artery bypass graft (U-CABG) surgery and postoperative acute kidney injury (AKI). We aimed to (1) analyze the impact of urgent CABG (U-CABG) on the incidence and severity of postoperative AKI, (2) estimate the influence of AKI after UCABG or elective CABG (E-CABG) on mortality and (3) identify risk factors for AKI depending on the urgency of operation. RESULTS: UCABG patients showed a higher incidence of AKI (49.8% vs. ECABG: 39.7%; pâ¯= 0.026), especially for higher AKI stages 2â¯+ 3. In-hospital mortality was higher in UCABG patients (12.6%) compared to ECABG patients (2.3%; pâ¯<â¯0.001). The impact of AKI on mortality did not differ, but showed a strong coherency between higher AKI stages (2â¯+ 3) and mortality (stage 1: OR 2.409, 95% CI 1.017-5.706; pâ¯= 0.046 vs. stage 2â¯+ 3: OR 5.577; 95% CI 2.033-15.3; pâ¯= 0.001). Univariate logistic regression analysis revealed that preoperative renal impairment, peripheral vascular disease and transfusion of more than two red blood cell concentrates were predictors for postoperative AKI in both groups. CONCLUSIONS: UCABG is a risk factor for postoperative AKI and even "mild" AKI leads to a significantly higher mortality. Hence, the prevention of modifiable risk factors might reduce the incidence of postoperative AKI and thus improve outcome.
Subject(s)
Acute Kidney Injury , Postoperative Complications , Acute Kidney Injury/epidemiology , Acute Kidney Injury/etiology , Cohort Studies , Coronary Artery Bypass/adverse effects , Humans , Postoperative Complications/etiology , Retrospective Studies , Risk FactorsABSTRACT
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease that leads to the death of upper and lower motor neurons. While most cases of ALS are sporadic, some of the familial forms of the disease are caused by mutations in the gene encoding for the RNA-binding protein FUS. Under physiological conditions, FUS readily phase separates into liquid-like droplets in vivo and in vitro. ALS-associated mutations interfere with this process and often result in solid-like aggregates rather than fluid condensates. Yet, whether cells recognize and triage aberrant condensates remains poorly understood, posing a major barrier to the development of novel ALS treatments. Using a combination of ALS-associated FUS mutations, optogenetic manipulation of FUS condensation, chemically induced stress, and pH-sensitive reporters of organelle acidity, we systematically characterized the cause-effect relationship between the material state of FUS condensates and the sequestering of lysosomes. From our data, we can derive three conclusions. First, regardless of whether we use wild-type or mutant FUS, expression levels (i.e., high concentrations) play a dominant role in determining the fraction of cells having soluble or aggregated FUS. Second, chemically induced FUS aggregates recruit LAMP1-positive structures. Third, mature, acidic lysosomes accumulate only at FUS aggregates but not at liquid-condensates. Together, our data suggest that lysosome-degradation machinery actively distinguishes between fluid and solid condensates. Unraveling these aberrant interactions and testing strategies to manipulate the autophagosome-lysosome axis provides valuable clues for disease intervention.
ABSTRACT
BACKGROUND: Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of transcriptomes, arising as a powerful tool for discovering and characterizing cell types and their developmental trajectories. However, scRNA-seq analysis is complex, requiring a continuous, iterative process to refine the data and uncover relevant biological information. A diversity of tools has been developed to address the multiple aspects of scRNA-seq data analysis. However, an easy-to-use web application capable of conducting all critical steps of scRNA-seq data analysis is still lacking. We present Asc-Seurat, a feature-rich workbench, providing an user-friendly and easy-to-install web application encapsulating tools for an all-encompassing and fluid scRNA-seq data analysis. Asc-Seurat implements functions from the Seurat package for quality control, clustering, and genes differential expression. In addition, Asc-Seurat provides a pseudotime module containing dozens of models for the trajectory inference and a functional annotation module that allows recovering gene annotation and detecting gene ontology enriched terms. We showcase Asc-Seurat's capabilities by analyzing a peripheral blood mononuclear cell dataset. CONCLUSIONS: Asc-Seurat is a comprehensive workbench providing an accessible graphical interface for scRNA-seq analysis by biologists. Asc-Seurat significantly reduces the time and effort required to analyze and interpret the information in scRNA-seq datasets.
Subject(s)
Single-Cell Analysis , Software , Cluster Analysis , Gene Expression Profiling , Leukocytes, Mononuclear , Sequence Analysis, RNAABSTRACT
BACKGROUND: Diagnostic errors have been attributed to cognitive biases (reasoning shortcuts), which are thought to result from fast reasoning. Suggested solutions include slowing down the reasoning process. However, slower reasoning is not necessarily more accurate than faster reasoning. In this study, we studied the relationship between time to diagnose and diagnostic accuracy. METHODS: We conducted a multi-center within-subjects experiment where we prospectively induced availability bias (using Mamede et al.'s methodology) in 117 internal medicine residents. Subsequently, residents diagnosed cases that resembled those bias cases but had another correct diagnosis. We determined whether residents were correct, incorrect due to bias (i.e. they provided the diagnosis induced by availability bias) or due to other causes (i.e. they provided another incorrect diagnosis) and compared time to diagnose. RESULTS: We did not successfully induce bias: no significant effect of availability bias was found. Therefore, we compared correct diagnoses to all incorrect diagnoses. Residents reached correct diagnoses faster than incorrect diagnoses (115 s vs. 129 s, p < .001). Exploratory analyses of cases where bias was induced showed a trend of time to diagnose for bias diagnoses to be more similar to correct diagnoses (115 s vs 115 s, p = .971) than to other errors (115 s vs 136 s, p = .082). CONCLUSIONS: We showed that correct diagnoses were made faster than incorrect diagnoses, even within subjects. Errors due to availability bias may be different: exploratory analyses suggest a trend that biased cases were diagnosed faster than incorrect diagnoses. The hypothesis that fast reasoning leads to diagnostic errors should be revisited, but more research into the characteristics of cognitive biases is important because they may be different from other causes of diagnostic errors.
Subject(s)
Internal Medicine , Problem Solving , Bias , Diagnostic Errors , HumansABSTRACT
Pulmonary vein isolation (PVI) using cryoenergy is safe and efficient for treatment of atrial fibrillation (AF). Pre-existing upper gastrointestinal (GI) pathologies have been shown to increase the risk for AF. Therefore, this study aimed at assessing incidental pathologies of the upper GI tract in patients scheduled for PVI and to analyse the impact of patients' characteristics on PVI safety outcome. In 71 AF patients, who participated in the MADE-PVI trial, oesophagogastroduodenoscopy and endosonography were prospectively performed directly before and the day after PVI to assess pre-existing upper GI pathologies and post-interventional occurrence of PVI-associated lesions. Subgroup analysis of the MADE-PVI trial identified clinically relevant incidental findings in 53 patients (74.6%) with age > 50 years being a significant risk factor. Pre-existing reflux oesophagitis increased risk for PVI-associated mediastinal oedema, while patients already treated with proton pump inhibitors (PPI) had significantly fewer mediastinal oedema. Our results suggest that AF patients with pre-existing reflux oesophagitis are at higher risk for PVI-associated mediastinal lesions, which is decreased in patients with constant PPI-treatment prior to PVI. Since PVI-associated mediastinal lesions are regarded as surrogate parameter for an increased risk of the fatal complication of an oesophago-atrial fistula, our findings hint at a beneficial effect of pre-interventional prophylactic PPI-treatment to reduce risk for PVI-associated complications.German Clinical Trials Register (DRKS00016006; date of registration: 17/12/2018).