AIxSuture: vision-based assessment of open suturing skills.

PURPOSE: Efficient and precise surgical skills are essential in ensuring positive patient outcomes. By continuously providing real-time, data driven, and objective evaluation of surgical performance, automated skill assessment has the potential to greatly improve surgical skill training. Whereas machine learning-based surgical skill assessment is gaining traction for minimally invasive techniques, this cannot be said for open surgery skills. Open surgery generally has more degrees of freedom when compared to minimally invasive surgery, making it more difficult to interpret. In this paper, we present novel approaches for skill assessment for open surgery skills. METHODS: We analyzed a novel video dataset for open suturing training. We provide a detailed analysis of the dataset and define evaluation guidelines, using state of the art deep learning models. Furthermore, we present novel benchmarking results for surgical skill assessment in open suturing. The models are trained to classify a video into three skill levels based on the global rating score. To obtain initial results for video-based surgical skill classification, we benchmarked a temporal segment network with both an I3D and a Video Swin backbone on this dataset. RESULTS: The dataset is composed of 314 videos of approximately five minutes each. Model benchmarking results are an accuracy and F1 score of up to 75 and 72%, respectively. This is similar to the performance achieved by the individual raters, regarding inter-rater agreement and rater variability. We present the first end-to-end trained approach for skill assessment for open surgery training. CONCLUSION: We provide a thorough analysis of a new dataset as well as novel benchmarking results for surgical skill assessment. This opens the doors to new advances in skill assessment by enabling video-based skill assessment for classic surgical techniques with the potential to improve the surgical outcome of patients.

De novo variants in RNF213 are associated with a clinical spectrum ranging from Leigh syndrome to early-onset stroke.

PURPOSE: RNF213, encoding a giant E3 ubiquitin ligase, has been recognized for its role as a key susceptibility gene for moyamoya disease. Case reports have also implicated specific variants in RNF213 with an early-onset form of moyamoya disease with full penetrance. We aimed to expand the phenotypic spectrum of monogenic RNF213-related disease and to evaluate genotype-phenotype correlations. METHODS: Patients were identified through reanalysis of exome sequencing data of an unselected cohort of unsolved pediatric cases and through GeneMatcher or ClinVar. Functional characterization was done by proteomics analysis and oxidative phosphorylation enzyme activities using patient-derived fibroblasts. RESULTS: We identified 14 individuals from 13 unrelated families with (de novo) missense variants in RNF213 clustering within or around the Really Interesting New Gene (RING) domain. Individuals presented either with early-onset stroke (n = 11) or with Leigh syndrome (n = 3). No genotype-phenotype correlation could be established. Proteomics using patient-derived fibroblasts revealed no significant differences between clinical subgroups. 3D modeling revealed a clustering of missense variants in the tertiary structure of RNF213 potentially affecting zinc-binding suggesting a gain-of-function or dominant negative effect. CONCLUSION: De novo missense variants in RNF213 clustering in the E3 RING or other regions affecting zinc-binding lead to an early-onset syndrome characterized by stroke or Leigh syndrome.

Effect of head-mounted displays on students' acquisition of surgical suturing techniques compared to an e-learning and tutor-led course: a randomized controlled trial.

BACKGROUND: Although surgical suturing is one of the most important basic skills, many medical school graduates do not acquire sufficient knowledge of it due to its lack of integration into the curriculum or a shortage of tutors. E-learning approaches attempt to address this issue but still rely on the involvement of tutors. Furthermore, the learning experience and visual-spatial ability appear to play a critical role in surgical skill acquisition. Virtual reality head-mounted displays (HMDs) could address this, but the benefits of immersive and stereoscopic learning of surgical suturing techniques are still unclear. MATERIAL AND METHODS: In this multi-arm randomized controlled trial, 150 novices participated. Three teaching modalities were compared: an e-learning course (monoscopic), an HMD-based course (stereoscopic, immersive), both self-directed and a tutor-led course with feedback. Suturing performance was recorded by video camera both before and after course participation (>26 h of video material) and assessed in a blinded fashion using the Objective Structured Assessment of Technical Skills (OSATS) Global Rating Score (GRS). Furthermore, the optical flow of the videos was determined using an algorithm. The number of sutures performed was counted, the visual-spatial ability was measured with the Mental Rotation Test (MRT), and courses were assessed with questionnaires. RESULTS: Students' self-assessment in the HMD-based course was comparable to that of the tutor-led course and significantly better than in the e-learning course ( P =0.003). Course suitability was rated best for the tutor-led course ( x̄ =4.8), followed by the HMD-based ( x̄ =3.6) and e-learning ( x̄ =2.5) courses. The median ΔGRS between courses was comparable ( P =0.15) at 12.4 (95% CI 10.0-12.7) for the e-learning course, 14.1 (95% CI 13.0-15.0) for the HMD-based course, and 12.7 (95% CI 10.3-14.2) for the tutor-led course. However, the ΔGRS was significantly correlated with the number of sutures performed during the training session ( P =0.002), but not with visual-spatial ability ( P =0.615). Optical flow ( R2 =0.15, P <0.001) and the number of sutures performed ( R2 =0.73, P <0.001) can be used as additional measures to GRS. CONCLUSION: The use of HMDs with stereoscopic and immersive video provides advantages in the learning experience and should be preferred over a traditional web application for e-learning. Contrary to expectations, feedback is not necessary for novices to achieve a sufficient level in suturing; only the number of surgical sutures performed during training is a good determinant of competence improvement. Nevertheless, feedback still enhances the learning experience. Therefore, automated assessment as an alternative feedback approach could further improve self-directed learning modalities. As a next step, the data from this study could be used to develop such automated AI-based assessments.

Human CARMIL2 deficiency underlies a broader immunological and clinical phenotype than CD28 deficiency.

Patients with inherited CARMIL2 or CD28 deficiency have defective T cell CD28 signaling, but their immunological and clinical phenotypes remain largely unknown. We show that only one of three CARMIL2 isoforms is produced and functional across leukocyte subsets. Tested mutant CARMIL2 alleles from 89 patients and 52 families impair canonical NF-κB but not AP-1 and NFAT activation in T cells stimulated via CD28. Like CD28-deficient patients, CARMIL2-deficient patients display recalcitrant warts and low blood counts of CD4+ and CD8+ memory T cells and CD4+ TREGs. Unlike CD28-deficient patients, they have low counts of NK cells and memory B cells, and their antibody responses are weak. CARMIL2 deficiency is fully penetrant by the age of 10 yr and is characterized by numerous infections, EBV+ smooth muscle tumors, and mucocutaneous inflammation, including inflammatory bowel disease. Patients with somatic reversions of a mutant allele in CD4+ T cells have milder phenotypes. Our study suggests that CARMIL2 governs immunological pathways beyond CD28.

Abatacept for treatment-refractory pediatric CTLA4-haploinsufficiency.

CTLA4-haploinsufficiency is a complex disease of immune dysregulation presenting with a broad spectrum of clinical manifestations. CTLA4-Fc fusion proteins such as abatacept have been described to alleviate immune dysregulation in several adult cases of CTLA4-haploinsufficiency. However, until now only few cases of pediatric CTLA4-haploinsufficiency treated with abatacept have been described. Here we present two pediatric cases of severe CTLA4-haploinsufficiency refractory to conventional immunosuppressive therapies that responded rapidly to treatment with abatacept. No side effects were observed during a follow-up period of 7-15 months. While one patient has successfully undergone HSCT the second patient continues to receive abatacept. Our cases demonstrate safe medium-term use of abatacept in the pediatric population.

Rubella Virus Infected Macrophages and Neutrophils Define Patterns of Granulomatous Inflammation in Inborn and Acquired Errors of Immunity.

Rubella virus (RuV) has recently been found in association with granulomatous inflammation of the skin and several internal organs in patients with inborn errors of immunity (IEI). The cellular tropism and molecular mechanisms of RuV persistence and pathogenesis in select immunocompromised hosts are not clear. We provide clinical, immunological, virological, and histological data on a cohort of 28 patients with a broad spectrum of IEI and RuV-associated granulomas in skin and nine extracutaneous tissues to further delineate this relationship. Combined immunodeficiency was the most frequent diagnosis (67.8%) among patients. Patients with previously undocumented conditions, i.e., humoral immunodeficiencies, a secondary immunodeficiency, and a defect of innate immunity were identified as being susceptible to RuV-associated granulomas. Hematopoietic cell transplantation was the most successful treatment in this case series resulting in granuloma resolution; steroids, and TNF-α and IL-1R inhibitors were moderately effective. In addition to M2 macrophages, neutrophils were identified by immunohistochemical analysis as a novel cell type infected with RuV. Four patterns of RuV-associated granulomatous inflammation were classified based on the structural organization of granulomas and identity and location of cell types harboring RuV antigen. Identification of conditions that increase susceptibility to RuV-associated granulomas combined with structural characterization of the granulomas may lead to a better understanding of the pathogenesis of RuV-associated granulomas and discover new targets for therapeutic interventions.

Benchmarking of long-read correction methods.

Third-generation sequencing technologies provided by Pacific Biosciences and Oxford Nanopore Technologies generate read lengths in the scale of kilobasepairs. However, these reads display high error rates, and correction steps are necessary to realize their great potential in genomics and transcriptomics. Here, we compare properties of PacBio and Nanopore data and assess correction methods by Canu, MARVEL and proovread in various combinations. We found total error rates of around 13% in the raw datasets. PacBio reads showed a high rate of insertions (around 8%) whereas Nanopore reads showed similar rates for substitutions, insertions and deletions of around 4% each. In data from both technologies the errors were uniformly distributed along reads apart from noisy 5' ends, and homopolymers appeared among the most over-represented kmers relative to a reference. Consensus correction using read overlaps reduced error rates to about 1% when using Canu or MARVEL after patching. The lowest error rate in Nanopore data (0.45%) was achieved by applying proovread on MARVEL-patched data including Illumina short-reads, and the lowest error rate in PacBio data (0.42%) was the result of Canu correction with minimap2 alignment after patching. Our study provides valuable insights and benchmarks regarding long-read data and correction methods.

Comparative transcriptome analysis of a Trichoplusia ni cell line reveals distinct host responses to intracellular and secreted protein products expressed by recombinant baculoviruses.

The baculovirus insect cell expression system has become a firmly established production platform in biotechnology. Various complex proteins, multi-subunit particles including veterinary and human vaccines are manufactured with this system on a commercial scale. Apart from baculovirus infected Spodoptera frugiperda (Sf9) cells, the Trichoplusia ni (HighFive) cell line is alternatively used as host organism. In this study, we explored the protein production capabilities of Tnms42 insect cells, a new derivative of HighFive, which is free of latent nodavirus infection. As a model system, a cytosolic (mCherry) and a secreted (hemagglutinin) protein were overexpressed in Tnms42 cells. The response of the host cells was followed in a time course experiment over the infection cycle by comparative transcriptome analysis (RNA-seq). As expected, the baculovirus infection per se had a massive impact on the host cell transcriptome, which was observed by the huge total number of differentially expressed transcripts (>14,000). Despite this severe overall cellular reaction, a specific response could be clearly attributed to the overexpression of secreted hemagglutinin, revealing limits in the secretory capacity of the host cell. About 400 significantly regulated transcripts were identified and assigned to biochemical pathways and gene ontology (GO) categories, all related to protein processing, folding and response to unfolded protein. The identification of relevant target genes will serve to design specific virus engineering concepts for improving the yield of proteins that are dependent on the secretory pathway.