Identification of a Master Regulator of Differentiation in Toxoplasma.

Toxoplasma gondii chronically infects a quarter of the world's population, and its recrudescence can cause life-threatening disease in immunocompromised individuals and recurrent ocular lesions in the immunocompetent. Acute-stage tachyzoites differentiate into chronic-stage bradyzoites, which form intracellular cysts resistant to immune clearance and existing therapies. The molecular basis of this differentiation is unknown, despite being efficiently triggered by stresses in culture. Through Cas9-mediated screening and single-cell profiling, we identify a Myb-like transcription factor (BFD1) necessary for differentiation in cell culture and in mice. BFD1 accumulates during stress and its synthetic expression is sufficient to drive differentiation. Consistent with its function as a transcription factor, BFD1 binds the promoters of many stage-specific genes and represents a counterpoint to the ApiAP2 factors that dominate our current view of parasite gene regulation. BFD1 provides a genetic switch to study and control Toxoplasma differentiation and will inform prevention and treatment of chronic infections.

Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics.

Ebola virus (EBOV) causes epidemics with high mortality yet remains understudied due to the challenge of experimentation in high-containment and outbreak settings. Here, we used single-cell transcriptomics and CyTOF-based single-cell protein quantification to characterize peripheral immune cells during EBOV infection in rhesus monkeys. We obtained 100,000 transcriptomes and 15,000,000 protein profiles, finding that immature, proliferative monocyte-lineage cells with reduced antigen-presentation capacity replace conventional monocyte subsets, while lymphocytes upregulate apoptosis genes and decline in abundance. By quantifying intracellular viral RNA, we identify molecular determinants of tropism among circulating immune cells and examine temporal dynamics in viral and host gene expression. Within infected cells, EBOV downregulates STAT1 mRNA and interferon signaling, and it upregulates putative pro-viral genes (e.g., DYNLL1 and HSPA5), nominating pathways the virus manipulates for its replication. This study sheds light on EBOV tropism, replication dynamics, and elicited immune response and provides a framework for characterizing host-virus interactions under maximum containment.

SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues.

There is pressing urgency to understand the pathogenesis of the severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2), which causes the disease COVID-19. SARS-CoV-2 spike (S) protein binds angiotensin-converting enzyme 2 (ACE2), and in concert with host proteases, principally transmembrane serine protease 2 (TMPRSS2), promotes cellular entry. The cell subsets targeted by SARS-CoV-2 in host tissues and the factors that regulate ACE2 expression remain unknown. Here, we leverage human, non-human primate, and mouse single-cell RNA-sequencing (scRNA-seq) datasets across health and disease to uncover putative targets of SARS-CoV-2 among tissue-resident cell subsets. We identify ACE2 and TMPRSS2 co-expressing cells within lung type II pneumocytes, ileal absorptive enterocytes, and nasal goblet secretory cells. Strikingly, we discovered that ACE2 is a human interferon-stimulated gene (ISG) in vitro using airway epithelial cells and extend our findings to in vivo viral infections. Our data suggest that SARS-CoV-2 could exploit species-specific interferon-driven upregulation of ACE2, a tissue-protective mediator during lung injury, to enhance infection.

Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity.

Acute myeloid leukemia (AML) is a heterogeneous disease that resides within a complex microenvironment, complicating efforts to understand how different cell types contribute to disease progression. We combined single-cell RNA sequencing and genotyping to profile 38,410 cells from 40 bone marrow aspirates, including 16 AML patients and five healthy donors. We then applied a machine learning classifier to distinguish a spectrum of malignant cell types whose abundances varied between patients and between subclones in the same tumor. Cell type compositions correlated with prototypic genetic lesions, including an association of FLT3-ITD with abundant progenitor-like cells. Primitive AML cells exhibited dysregulated transcriptional programs with co-expression of stemness and myeloid priming genes and had prognostic significance. Differentiated monocyte-like AML cells expressed diverse immunomodulatory genes and suppressed T cell activity in vitro. In conclusion, we provide single-cell technologies and an atlas of AML cell states, regulators, and markers with implications for precision medicine and immune therapies. VIDEO ABSTRACT.

The cellular architecture of the antimicrobial response network in human leprosy granulomas.

Granulomas are complex cellular structures composed predominantly of macrophages and lymphocytes that function to contain and kill invading pathogens. Here, we investigated the single-cell phenotypes associated with antimicrobial responses in human leprosy granulomas by applying single-cell and spatial sequencing to leprosy biopsy specimens. We focused on reversal reactions (RRs), a dynamic process whereby some patients with disseminated lepromatous leprosy (L-lep) transition toward self-limiting tuberculoid leprosy (T-lep), mounting effective antimicrobial responses. We identified a set of genes encoding proteins involved in antimicrobial responses that are differentially expressed in RR versus L-lep lesions and regulated by interferon-γ and interleukin-1ß. By integrating the spatial coordinates of the key cell types and antimicrobial gene expression in RR and T-lep lesions, we constructed a map revealing the organized architecture of granulomas depicting compositional and functional layers by which macrophages, T cells, keratinocytes and fibroblasts can each contribute to the antimicrobial response.

Evolution, biomechanics, and neurobiology converge to explain selective finger motor control.

Humans use their fingers to perform a variety of tasks, from simple grasping to manipulating objects, to typing and playing musical instruments, a variety wider than any other species. The more sophisticated the task, the more it involves individuated finger movements, those in which one or more selected fingers perform an intended action while the motion of other digits is constrained. Here we review the neurobiology of such individuated finger movements. We consider their evolutionary origins, the extent to which finger movements are in fact individuated, and the evolved features of neuromuscular control that both enable and limit individuation. We go on to discuss other features of motor control that combine with individuation to create dexterity, the impairment of individuation by disease, and the broad extent of capabilities that individuation confers on humans. We comment on the challenges facing the development of a truly dexterous bionic hand. We conclude by identifying topics for future investigation that will advance our understanding of how neural networks interact across multiple regions of the central nervous system to create individuated movements for the skills humans use to express their cognitive activity.

Multimodal profiling of lung granulomas in macaques reveals cellular correlates of tuberculosis control.

Mycobacterium tuberculosis lung infection results in a complex multicellular structure: the granuloma. In some granulomas, immune activity promotes bacterial clearance, but in others, bacteria persist and grow. We identified correlates of bacterial control in cynomolgus macaque lung granulomas by co-registering longitudinal positron emission tomography and computed tomography imaging, single-cell RNA sequencing, and measures of bacterial clearance. Bacterial persistence occurred in granulomas enriched for mast, endothelial, fibroblast, and plasma cells, signaling amongst themselves via type 2 immunity and wound-healing pathways. Granulomas that drove bacterial control were characterized by cellular ecosystems enriched for type 1-type 17, stem-like, and cytotoxic T cells engaged in pro-inflammatory signaling networks involving diverse cell populations. Granulomas that arose later in infection displayed functional characteristics of restrictive granulomas and were more capable of killing Mtb. Our results define the complex multicellular ecosystems underlying (lack of) granuloma resolution and highlight host immune targets that can be leveraged to develop new vaccine and therapeutic strategies for TB.

Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies.

High-throughput single-cell RNA-sequencing (scRNA-seq) methodologies enable characterization of complex biological samples by increasing the number of cells that can be profiled contemporaneously. Nevertheless, these approaches recover less information per cell than low-throughput strategies. To accurately report the expression of key phenotypic features of cells, scRNA-seq platforms are needed that are both high fidelity and high throughput. To address this need, we created Seq-Well S3 ("Second-Strand Synthesis"), a massively parallel scRNA-seq protocol that uses a randomly primed second-strand synthesis to recover complementary DNA (cDNA) molecules that were successfully reverse transcribed but to which a second oligonucleotide handle, necessary for subsequent whole transcriptome amplification, was not appended due to inefficient template switching. Seq-Well S3 increased the efficiency of transcript capture and gene detection compared with that of previous iterations by up to 10- and 5-fold, respectively. We used Seq-Well S3 to chart the transcriptional landscape of five human inflammatory skin diseases, thus providing a resource for the further study of human skin inflammation.

Optimal reaching subject to computational and physical constraints reveals structure of the sensorimotor control system.

Optimal feedback control provides an abstract framework describing the architecture of the sensorimotor system without prescribing implementation details such as what coordinate system to use, how feedback is incorporated, or how to accommodate changing task complexity. We investigate how such details are determined by computational and physical constraints by creating a model of the upper limb sensorimotor system in which all connection weights between neurons, feedback, and muscles are unknown. By optimizing these parameters with respect to an objective function, we find that the model exhibits a preference for an intrinsic (joint angle) coordinate representation of inputs and feedback and learns to calculate a weighted feedforward and feedback error. We further show that complex reaches around obstacles can be achieved by augmenting our model with a path-planner based on via points. The path-planner revealed "avoidance" neurons that encode directions to reach around obstacles and "placement" neurons that make fine-tuned adjustments to via point placement. Our results demonstrate the surprising capability of computationally constrained systems and highlight interesting characteristics of the sensorimotor system.

Prevention of tuberculosis in macaques after intravenous BCG immunization.

Mycobacterium tuberculosis (Mtb) is the leading cause of death from infection worldwide1. The only available vaccine, BCG (Bacillus Calmette-Guérin), is given intradermally and has variable efficacy against pulmonary tuberculosis, the major cause of mortality and disease transmission1,2. Here we show that intravenous administration of BCG profoundly alters the protective outcome of Mtb challenge in non-human primates (Macaca mulatta). Compared with intradermal or aerosol delivery, intravenous immunization induced substantially more antigen-responsive CD4 and CD8 T cell responses in blood, spleen, bronchoalveolar lavage and lung lymph nodes. Moreover, intravenous immunization induced a high frequency of antigen-responsive T cells across all lung parenchymal tissues. Six months after BCG vaccination, macaques were challenged with virulent Mtb. Notably, nine out of ten macaques that received intravenous BCG vaccination were highly protected, with six macaques showing no detectable levels of infection, as determined by positron emission tomography-computed tomography imaging, mycobacterial growth, pathology and granuloma formation. The finding that intravenous BCG prevents or substantially limits Mtb infection in highly susceptible rhesus macaques has important implications for vaccine delivery and clinical development, and provides a model for defining immune correlates and mechanisms of vaccine-elicited protection against tuberculosis.

Quantitative Metabolomics and Lipoprotein Analysis of PDAC Patients Suggests Serum Marker Categories for Pancreatic Function, Pancreatectomy, Cancer Metabolism, and Systemic Disturbances.

Pancreatic ductal adenocarcinoma (PDAC) is difficult to diagnose in the early stages and lacks reliable biomarkers. The scope of this project was to establish quantitative nuclear magnetic resonance (NMR) spectroscopy to comprehensively study blood serum alterations in PDAC patients. Serum samples from 34 PDAC patients obtained before and after pancreatectomy as well as 83 age- and sex-matched control samples from healthy donors were analyzed with in vitro diagnostics research (IVDr) proton NMR spectroscopy at 600 MHz. Uni- and multivariate statistics were applied to identify significant biofluid alterations. We identified 29 significantly changed metabolites and 98 lipoproteins when comparing serum from healthy controls with those of PDAC patients. The most prominent features were assigned to (i) markers of pancreatic function (e.g., glucose and blood triglycerides), (ii) markers related to surgery (e.g., ketone bodies and blood cholesterols), (iii) PDAC-associated markers (e.g., amino acids and creatine), and (iv) markers for systemic disturbances in PDAC (e.g., gut metabolites DMG, TMAO, DMSO2, and liver lipoproteins). Quantitative serum NMR spectroscopy is suited as a diagnostic tool to investigate PDAC. Remarkably, 2-hydroxybutyrate (2-HB) as a previously suggested marker for insulin resistance was found in extraordinarily high levels only after pancreatectomy, suggesting this metabolite is the strongest marker for pancreatic loss of function.

Cefadroxil and cephalexin pharmacokinetics and pharmacodynamics in children with musculoskeletal infections.

Cephalexin, a first-generation cephalosporin, is the first-line oral therapy for children with musculoskeletal infections due to methicillin-susceptible Staphylococcus aureus (MSSA). Cefadroxil, a similar first-generation cephalosporin, is an attractive alternative to cephalexin given its longer half-life. In this study, we describe the comparative pharmacokinetics (PK) and pharmacodynamics (PD) of cephalexin and cefadroxil in children with musculoskeletal infections. Children aged 6 months to 18 years with a musculoskeletal infection were enrolled in a prospective, open-label, crossover PK study and given single oral doses of cefadroxil (50-75 mg/kg up to 2,000 mg) and cephalexin (50 mg/kg up to 1,375 mg). Population PK models were developed and used for dosing simulations. Our primary PD target was the achievement of free antibiotic concentrations above the minimum inhibitory concentration (fT >MIC) for 40% of the day for MICs ≤ 4 mg/L. PK of cephalexin (n = 15) and cefadroxil (n = 14) were best described using a one-compartment, first-order absorption model, with a lag time component for cefadroxil. PK parameters were notable for cefadroxil's longer half-life (1.61 h) than cephalexin's (1.10 h). For pediatric weight bands, our primary PD target was achieved by cephalexin 25 mg/kg/dose, maximum 750 mg/dose, administered three times daily and cefadroxil 40 mg/kg/dose, maximum 1,500 mg/dose, administered twice daily. More aggressive dosing was required to achieve higher PD targets. Among children with musculoskeletal infections, oral cephalexin and cefadroxil achieved PD targets for efficacy against MSSA. Given less frequent dosing, twice-daily cefadroxil should be further considered as an alternative to cephalexin for oral step-down therapy for serious infections due to MSSA.

Participation rate and yield of two home-based screening methods to detect increased albuminuria in the general population in the Netherlands (THOMAS): a prospective, randomised, open-label implementation study.

BACKGROUND: Chronic kidney disease (CKD) has a rising global prevalence and is expected to become the fifth leading cause of death by 2030. Increased albuminuria defines the early stages of CKD and is among the strongest risk factors for progressive CKD and cardiovascular disease. The value of population screening for albuminuria to detect CKD in an early phase has yet to be studied. We aimed to evaluate the effectiveness of two home-based albuminuria population screening methods. METHODS: Towards Home-based Albuminuria Screening (THOMAS) was a prospective, randomised, open-label implementation study that invited Dutch adults aged 45-80 years for albuminuria screening. Individuals were randomly assigned (1:1) to screening by applying either a urine collection device (UCD) that was sent by post to a central laboratory for measurement of the albumin-to-creatinine ratio (ACR) by immunoturbidimetry or to screening via a smartphone application that measures the ACR with a dipstick method at home. Randomisation was done with a four-block method via a web-based system and was stratified by age, sex, and socioeconomic status. If two or more individuals per household were invited to participate, these individuals were randomly assigned to the same group. In case of confirmed increased albuminuria at home, participants were invited for an elaborate screening in a regional hospital (Amphia Hospital, Breda, Netherlands) for CKD and cardiovascular risk factors. When abnormalities were found, participants were referred to their general practitioner for treatment. The primary outcomes were the participation rate and yield of the home-based screening and elaborate screening. Participation rate was assessed in the intention-to-screen population (ie, all participants who were invited for the home-based screening or elaborate screening). Yield was assessed in the per-protocol population (ie, all individuals who participated in the home-based screening or elaborate screening). An exploratory analysis assessed the sensitivity and specificity of both home-based screening methods. To this end, an additional quantitative ACR test was performed among people participating in the elaborate screening, and a substudy was performed among participants with a first negative home-based screening test, who were invited for an additional test. The study is registered with ClinicalTrials.gov, NCT04295889. FINDINGS: 15 074 participants were enrolled between Nov 14, 2019, and March 19, 2021. 7552 (50·1%) were randomly assigned to home-based albuminuria screening by the UCD method and 7522 (49·9%) were assigned to albuminuria screening by the smartphone application method. The participation rate of the home-based screening was 4484 (59·4% [95% CI 58·3-60·5]) of the 7552 invited individuals for the UCD method and 3336 (44·3% [43·2-45·5]) of 7522 invited individuals for the smartphone application method (p<0·0001). Increased ACR was confirmed by home-based testing in 150 (3·3% [95% CI 2·9-3·9]) of 4484 individuals for the UCD method and 171 (5·1% [4·4-5·9]) of 3336 indivduals for the smartphone application method. 124 (82·7% [95% CI 75·8-87·9]) of 150 individuals assigned to the UCD method and 142 (83·0% [76·7-87·9]) of 171 participants assigned to the smartphone application method attended the elaborate screening. Sensitivity to detect increased ACR was 96·6% (95% CI 91·5-99·1) for the UCD method and 98·1% (89·9-99·9) for the smartphone application method, and specificity was 97·3% (94·7-98·8) for the UCD method and 67·9% (62·0-73·3) for the smartphone application method, indicating that the test characteristics of only the UCD method were sufficient for screening. Albuminuria, hypertension, hypercholesterolaemia, and decreased kidney function were newly diagnosed in 77 (62·1%), 44 (35·5%), 30 (24·2%), and 27 (21·8%) of 124 participants for the UCD method, respectively. Of the 124 participants assigned to the UCD method who completed elaborate screening, 111 (89·5%) were referred to their general practitioner for treatment because of newly diagnosed CKD or cardiovascular disease risk factors or known risk factors outside the target range. INTERPRETATION: Home-based screening of the general population for increased ACR using a UCD had a high participation rate and correctly identified individuals with increased albuminuria and yet unknown or known but outside target range CKD and cardiovascular risk factors. By contrast, the smartphone application method had a lower at-home participation rate than the UCD method and the test specificity was too low to accurately assess individuals for risk factors during the elaborate screening. The UCD screening strategy could allow for an early start of treatment to prevent progressive kidney function loss and cardiovascular disease in patients with CKD. FUNDING: Dutch Kidney Foundation, Top Sector Life Sciences & Health of the Dutch Ministry of Economic Affairs.

Liver regeneration after portal and hepatic vein embolization improves overall survival compared with portal vein embolization alone: mid-term survival analysis of the multicentre DRAGON 0 cohort.

BACKGROUND: The purpose of this study was to compare 3-year overall survival after simultaneous portal (PVE) and hepatic vein (HVE) embolization versus PVE alone in patients undergoing liver resection for primary and secondary cancers of the liver. METHODS: In this multicentre retrospective study, all DRAGON 0 centres provided 3-year follow-up data for all patients who had PVE/HVE or PVE, and were included in DRAGON 0 between 2016 and 2019. Kaplan-Meier analysis was undertaken to assess 3-year overall and recurrence/progression-free survival. Factors affecting survival were evaluated using univariable and multivariable Cox regression analyses. RESULTS: In total, 199 patients were included from 7 centres, of whom 39 underwent PVE/HVE and 160 PVE alone. Groups differed in median age (P = 0.008). As reported previously, PVE/HVE resulted in a significantly higher resection rate than PVE alone (92 versus 68%; P = 0.007). Three-year overall survival was significantly higher in the PVE/HVE group (median survival not reached after 36 months versus 20 months after PVE; P = 0.004). Univariable and multivariable analyses identified PVE/HVE as an independent predictor of survival (univariable HR 0.46, 95% c.i. 0.27 to 0.76; P = 0.003). CONCLUSION: Overall survival after PVE/HVE is substantially longer than that after PVE alone in patients with primary and secondary liver tumours.

Bending a Cumulene with Electrons: Stepwise Chemical Reduction and Structural Study of a Tetraaryl[4]Cumulene.

Chemical reduction of a [4]cumulene with cesium metal was explored, and the structural changes stemming from electron acquisition are detailed using X-ray crystallography. It is found that the [4]cumulene undergoes dramatic geometric changes upon stepwise reduction, including bending of the cumulenic core and twisting of the endgroups from orthogonal to planar. The structural deformation is consistent with early theoretical reports that suggest that the twisting should occur upon reduction of both even and odd [n]cumulenes. The current results, on the other hand, are inconsistent with a previous experimental study of a [3]cumulene in which the predicted twisting is not observed upon reduction. DFT calculations reveal that the barrier to deformation is an order of magnitude lower in a [3]cumulene than a [4]cumulene, allowing the barrier to be overcome in the solid-state.

Third-trimester fetoscopic ablation therapy for types II and III vasa previa.

BACKGROUND: Vasa previa is an obstetrical condition in which fetal vessels located near the cervix traverse the fetal membranes unprotected by underlying placenta. Type I vasa previa arises directly from a velamentous cord root, whereas types II and III arise from an accessory lobe or a distal lobe of the same placenta, respectively. Fetoscopic laser ablation for types II and III vasa previa is a novel therapeutic option with benefits that include surgical resolution of the vasa previa, avoidance of prolonged hospitalization, and opportunity for a term vaginal delivery. The potential risks of fetoscopy can be mitigated by delaying laser surgery until a gestational age of 31 to 33 weeks, immediately before anticipated hospitalized surveillance. OBJECTIVE: This study aimed to assess feasibility and outcomes of types II and III vasa previa patients treated via fetoscopic laser ablation in the third trimester. STUDY DESIGN: This is a retrospective study of singleton pregnancies with types II and III vasa previa treated with fetoscopic laser ablation at a gestational age ≥31 weeks at a single center between 2006 and 2022. Pregnancy and newborn outcomes were assessed. Continuous variables are expressed as mean±standard deviation. RESULTS: Of 84 patients referred for vasa previa, 57 did not undergo laser ablation: 19 either had no or resolved vasa previa, 25 had type I vasa previa (laser-contraindicated), and 13 had type II or III vasa previa but declined laser treatment. Of the remaining 27 patients who underwent laser ablation, 7 were excluded (laser performed at <31 weeks and/or twins), leaving 20 study patients. The mean gestational age at fetoscopic laser ablation was 32.0±0.6 weeks, and total operative time was 62.1±19.6 minutes. There were no perioperative complications. All patients had successful occlusion of the vasa previa vessels (1 required a second procedure). All patients were subsequently managed as outpatients. The mean gestational age at delivery was 37.2±1.8 weeks, the mean birthweight was 2795±465 g, and 70% delivered vaginally. Neonatal intensive care unit admission occurred in 3 cases: 1 for respiratory distress syndrome and 2 for hyperbilirubinemia requiring phototherapy. There were no cases of neonatal transfusion, intraventricular hemorrhage, sepsis, patent ductus arteriosus, or death. CONCLUSION: Laser ablation for types II and III vasa previa at 31 to 33 gestational weeks was technically achievable and resulted in favorable outcomes.

Changes in the epidemiology of kidney replacement therapy across Europe in 2020 - the first year of the COVID-19 pandemic: an ERA Registry study.

BACKGROUND: In 2020, the COVID-19 pandemic caused disruptions in kidney replacement therapy (KRT) services worldwide. The aim of this study was to assess the effect of the COVID-19 pandemic in 2020 on the incidence of KRT, kidney transplantation activity, mortality and prevalence of KRT across Europe. METHODS: Patients receiving KRT were included from 17 countries providing data to the European Renal Association Registry. The epidemiology of KRT in 2020 was compared with average data from the period 2017-2019. Also changes occurring during the first and second wave of the pandemic were explored. RESULTS: The incidence of KRT was 6.2% lower in 2020 compared with 2017-2019, with the lowest point (-22.7%) during the first wave in April. The decrease varied across countries, was smaller in males (-5.2%) than in females (-8.2%), and was moderate for peritoneal dialysis (-3.7%) and haemodialysis (-5.4%), but substantial for pre-emptive kidney transplantation (-23.6%). The kidney transplantation rate decreased by 22.5%, reaching a nadir of -80.1% during the first wave, and most for living donor kidney transplants (-30.5%). While in most countries the kidney transplantation rate decreased, in the Nordic/Baltic countries and Greece there was no clear decline. In dialysis patients, mortality increased by 11.4%, and was highest in those aged 65-74 years (16.1%), in those with diabetes as primary renal disease (15.1%), and in those on haemodialysis (12.4%). In transplant recipients, the mortality was 25.8% higher, but there were no subgroups that stood out. In contrast to the rising prevalence of KRT observed over the past decades across Europe, the prevalence at the end of 2020 (N=317787) resembled that of 2019 (N=317077). CONCLUSION: The COVID-19 pandemic has had a substantial impact on the incidence of KRT, kidney transplant activity, mortality of KRT, and prevalence of KRT in Europe with variations across countries.

The applicability of the central line-associated bloodstream infection (CLABSI) criteria for the evaluation of bacteremia episodes in pediatric oncology patients.

BACKGROUND: The aim of this study was to investigate the applicability of the central line-associated bloodstream infection (CLABSI) criteria of the Centers for Disease Control and Prevention in pediatric oncology patients. METHODS: Bacteremia episodes from 2020 to 2022 from a prospective cohort of pediatric oncology patients with a central venous catheter were included. Episodes were classified by three medical experts following the CLABSI criteria as either a CLABSI or non-CLABSI (i.e., contamination, other infection source, or mucosal barrier injury-laboratory confirmed bloodstream infection (MBI-LCBI)). Subsequently, they were asked if and why they (dis)agreed with this diagnosis following the criteria. The primary outcome was the percentage of episodes where the experts clinically disagreed with the diagnosis given following the CLABSI criteria. RESULTS: Overall, 84 bacteremia episodes in 71 patients were evaluated. Following the CLABSI criteria, 34 (40%) episodes were classified as CLABSIs and 50 (60%) as non-CLABSIs. In 11 (13%) cases the experts clinically disagreed with the diagnosis following the CLABSI criteria. The discrepancy between the CLABSI criteria and clinical diagnosis was significant; McNemar's test p < .01. Disagreement by the experts with the CLABSI criteria mostly occurred when the experts found an MBI-LCBI a more plausible cause of the bacteremia than a CLABSI due to the presence of a gram negative bacteremia (Pseudomonas aeruginosa n = 3) and/or mucositis. CONCLUSIONS: A discrepancy between the CLABSI criteria and the evaluation of the experts was observed. Adding Pseudomonas aeruginosa as an MBI pathogen and incorporating the presence of mucositis in the MBI-LCBI criteria, might increase the applicability.

Automated abdominal CT contrast phase detection using an interpretable and open-source artificial intelligence algorithm.

OBJECTIVES: To develop and validate an open-source artificial intelligence (AI) algorithm to accurately detect contrast phases in abdominal CT scans. MATERIALS AND METHODS: Retrospective study aimed to develop an AI algorithm trained on 739 abdominal CT exams from 2016 to 2021, from 200 unique patients, covering 1545 axial series. We performed segmentation of five key anatomic structures-aorta, portal vein, inferior vena cava, renal parenchyma, and renal pelvis-using TotalSegmentator, a deep learning-based tool for multi-organ segmentation, and a rule-based approach to extract the renal pelvis. Radiomics features were extracted from the anatomical structures for use in a gradient-boosting classifier to identify four contrast phases: non-contrast, arterial, venous, and delayed. Internal and external validation was performed using the F1 score and other classification metrics, on the external dataset "VinDr-Multiphase CT". RESULTS: The training dataset consisted of 172 patients (mean age, 70 years ± 8, 22% women), and the internal test set included 28 patients (mean age, 68 years ± 8, 14% women). In internal validation, the classifier achieved an accuracy of 92.3%, with an average F1 score of 90.7%. During external validation, the algorithm maintained an accuracy of 90.1%, with an average F1 score of 82.6%. Shapley feature attribution analysis indicated that renal and vascular radiodensity values were the most important for phase classification. CONCLUSION: An open-source and interpretable AI algorithm accurately detects contrast phases in abdominal CT scans, with high accuracy and F1 scores in internal and external validation, confirming its generalization capability. CLINICAL RELEVANCE STATEMENT: Contrast phase detection in abdominal CT scans is a critical step for downstream AI applications, deploying algorithms in the clinical setting, and for quantifying imaging biomarkers, ultimately allowing for better diagnostics and increased access to diagnostic imaging. KEY POINTS: Digital Imaging and Communications in Medicine labels are inaccurate for determining the abdominal CT scan phase. AI provides great help in accurately discriminating the contrast phase. Accurate contrast phase determination aids downstream AI applications and biomarker quantification.

Direct correlation of MR-DWI and histopathology of Wilms' tumours through a patient-specific 3D-printed cutting guide.

OBJECTIVES: The International Society of Paediatric Oncology-Renal Tumour Study Group (SIOP-RTSG) discourages invasive procedures to determine the histology of paediatric renal neoplasms at diagnosis. Therefore, the histological subtype of Wilms' tumours (WT) is unknown at the start of neoadjuvant chemotherapy. MR-DWI shows potential value as a non-invasive biomarker through apparent diffusion coefficients (ADCs). This study aimed to describe MR characteristics and ADC values of paediatric renal tumours to differentiate subtypes. MATERIALS AND METHODS: Children with a renal tumour undergoing surgery within the SIOP-RTSG 2016-UMBRELLA protocol were prospectively included between May 2021 and 2023. In the case of a total nephrectomy, a patient-specific cutting guide based on the neoadjuvant MR was 3D-printed, allowing a correlation between imaging and histopathology. Whole-tumour volumes and ADC values were statistically compared with the Mann-Whitney U-test. Direct correlation on the microscopic slide level was analysed through mixed model analysis. RESULTS: Fifty-nine lesions of 54 patients (58% male, median age 3.0 years (range 0-17.7 years)) were included. Forty-four lesions involved a WT. Stromal type WT showed the lowest median decrease in volume after neoadjuvant chemotherapy (48.1 cm3, range 561.5-(+)332.7 cm3, p = 0.035). On a microscopic slide level (n = 240 slides) after direct correlation through the cutting guide, stromal areas showed a significantly higher median ADC value compared to epithelial and blastemal foci (p < 0.001). With a cut-off value of 1.195 * 10-3 mm2/s, sensitivity, and specificity were 95.2% (95% confidence interval 87.6-98.4%) and 90.5% (95% confidence interval 68.2-98.3%), respectively. CONCLUSION: Correlation between histopathology and MR-DWI through a patient-specific 3D-printed cutting guide resulted in significant discrimination of stromal type WT from epithelial and blastemal subtypes. CLINICAL RELEVANCE STATEMENT: Stromal Wilms' tumours could be discriminated from epithelial- and blastemal lesions based on high apparent diffusion coefficient values and limited decrease in volume after neoadjuvant chemotherapy. This may aid in future decision-making, especially concerning discrimination between low- and high-risk neoplasms. KEY POINTS: MR-DWI shows potential value as a non-invasive biomarker in paediatric renal tumours. The patient-specific cutting guide leads to a correlation between apparent diffusion coefficient values and Wilms' tumour subtype. Stromal areas could be discriminated from epithelial and blastemal foci in Wilms' tumours based on apparent diffusion coefficient values.