Whether and When does Endoscopy Domain Pretraining Make Sense?

Automated endoscopy video analysis is a challenging task in medical computer vision, with the primary objective of assisting surgeons during procedures. The difficulty arises from the complexity of surgical scenes and the lack of a sufficient amount of annotated data. In recent years, large-scale pretraining has shown great success in natural language processing and computer vision communities. These approaches reduce the need for annotated data, which is always a concern in the medical domain. However, most works on endoscopic video understanding use models pretrained on natural images, creating a domain gap between pretraining and finetuning. In this work, we investigate the need for endoscopy domain-specific pretraining based on downstream objectives. To this end, we first collect Endo700k, the largest publicly available corpus of endoscopic images, extracted from nine public Minimally Invasive Surgery (MIS) datasets. Endo700k comprises more than 700,000 unannotated raw images. Next, we introduce EndoViT, an endoscopy pretrained Vision Transformer (ViT). Through ablations, we demonstrate that domain-specific pretraining is particularly beneficial for more complex downstream tasks, such as Action Triplet Detection, and less effective and even unnecessary for simpler tasks, such as Surgical Phase Recognition. We will release both our code and pretrained models upon acceptance to facilitate further research in this direction

Dynamic Scene Graph Representation for Surgical Video

Surgical videos captured from microscopic or endoscopic imaging devices are rich but complex sources of information, depicting different tools and anatomical structures utilized during an extended amount of time. Despite containing crucial workflow information and being commonly recorded in many procedures, usage of surgical videos for automated surgical workflow understanding is still limited. In this work, we exploit scene graphs as a more holistic, semantically meaningful and human-readable way to represent surgical videos while encoding all anatomical structures, tools, and their interactions. To properly evaluate the impact of our solutions, we create a scene graph dataset from semantic segmentations from the CaDIS and CATARACTS datasets. We demonstrate that scene graphs can be leveraged through the use of graph convolutional networks (GCNs) to tackle surgical downstream tasks such as surgical workflow recognition with competitive performance. Moreover, we demonstrate the benefits of surgical scene graphs regarding the explainability and robustness of model decisions, which are crucial in the clinical setting

The Formation and Coarsening of the Concertina Pattern

The concertina is a magnetization pattern in elongated thin-film elements of a soft material. It is a ubiquitous domain pattern that occurs in the process of magnetization reversal in direction of the long axis of the small element. Van den Berg argued that this pattern grows out of the flux closure domains as the external field is reduced. Based on experimental observations and theory, we argue that in sufficiently elongated thin-film elements, the concertina pattern rather bifurcates from an oscillatory buckling mode. Using a reduced model derived by asymptotic analysis and investigated by numerical simulation, we quantitatively predict the average period of the concertina pattern and qualitatively predict its hysteresis. In particular, we argue that the experimentally observed coarsening of the concertina pattern is due to secondary bifurcations related to an Eckhaus instability. We also link the concertina pattern to the magnetization ripple and discuss the effect of a weak (crystalline or induced) anisotropy

Magnetic resonance imaging evaluation of Yukatan minipig brains for neurotherapy applications

Magnetic resonance imaging (MRI) of six Yukatan minipig brains was performed. The animals were placed in stereotaxic conditions currently used in experiments. To allow for correctpositioning of the animal in the MRI instrument, landmarks were previously traced on the snout of the pig. To avoid movements, animal were anesthetized. The animals were placed in a prone position in a Siemens Magnetom Avanto 1.5 System with a head coil. Axial T2-weighted and sagittal T1-weighted MRI images were obtained from each pig. Afterwards, the brains of the pigs were fixed and cut into axial sections. Histologic and MR images were compared. The usefulness of this technique is discussed

Characterization of gastrointestinal transit and luminal conditions in pigs using a telemetric motility capsule

Within preclinical research, the pig has become an important model in regulatory toxicology and pharmacokinetics, to assess oral dosage forms and to compare different formulation strategies. In addition, there are emerging application of the pig model to asses clinical dosing conditions in the fasted and fed state. In this study, the gastrointestinal transit conditions in male landrace pigs were studied with a telemetric motility capsule under fasted and postprandial conditions. The whole gut transit time (WGTT) was determined by administering a SmartPill® capsule to four landrace pigs, under both fasted and fed state conditions in a cross-over study design. Overall, this study found that small intestinal transit in landrace pigs ranged from 2.3 – 4.0 h, and was broadly similar to reported human estimates and was not affected by the intake conditions. Gastric emptying was highly variable and prolonged in landrace pigs ranging from 20 – 233 h and up to 264 h in one specific case. Under dynamic conditions pigs have a low gastric pH comparable to humans, however a high variability under fasted conditions could be observed. The comparison of the data from this study with a recent similar study in beagle dogs revealed major differences between gastric maximum pressures observed in landrace pigs and dogs. In the porcine stomach maximum pressures of up to 402 mbar were observed, which are comparable to reported human data. Intestinal maximum pressures in landrace pigs were in the same range as in humans. Overall, the study provides new insights of gastrointestinal conditions in landrace pigs, which can lead to more accurate interpretation of in vivo results obtained of pharmacokinetic studies in preclinical models. While small intestinal transit conditions, GI pH and pressures were similar to humans, the prolonged gastric emptying observed in pigs need to be considered in assessing the suitability of the pig model for assessing in vivo performance of large non-disintegrated oral drug products.

Metropolis revisited: dialectic of enlightenment, modernity and architectural modernizm

Theodor Adorno ve Max Horkheimer, 'Aydınlanma'nın Diyalektiği: Felsefi Fragmanlar' (1947) adlı yapıtlarında, Aydınlanma projesinin yapısı gereği totaliter olduğunu ve mitolojiyi insan düşüncesinden kovmuş olmasına rağmen kendisinin mite gerilediğini öne sürmektedirler. Aydınlanma paradigmasının ürünü olan birer sanat dalı olarak erken 20. yüzyıl sineması ve mimarlık, Adorno ve Horkheimer'in bu savlarını doğrulamaktadırlar. Fritz Lang'in Metropolis (1927) adlı filmi; bir paradig- ma değişimi olarak Aydınlanma'nın, tarihsel bir dönem olarak Modernite'nin ve bu tarihsel döneme özgü bir üslup olarak Modern Mimari hareketin birbirleri ile ilişkilerinin çözümlenebilmesine olanak sağlayan çok katmanlı bir anlamsal yapı- ya sahiptir. Filmde Aydınlanma-mitoloji ile Modern Mimari-tarihsel içerik diyalektikleri paralel olarak işlenmiştir. Filmdeki, Metropolis'in makine estetiğine dayalı fütüristik ütopik mimarisi ile distopik tekno-totaliter toplumsal düzen arasındaki gerilim, gerçekte tarihsel üsluplardan yararlanmayı reddeden Modern Mimari hareketin ütopik karakteri ile mitoloji olarak tarihsel birikim arasındaki gerilimi yansıtmaktadır. Theodor Adorno and Max Horkheimer asserted that the project of enlightenment which itself is already totalitarian ai- med to overthrow the myths from the human mind and to install human beings as masters reverted to mythology at the end, in their master work 'Dialectic of Enlightment: Philosophical Fragments' (1947). As artistic products of Enlightment Project, cinema and architecture of early twentieth century affirmed Adorno and Horkheimer's thesis. Fritz Lang's Metro- polis (1927)'s multi-layered messages enables us to comprehend the relationships between Enlightment as a paratigmatic change, Modernity as a historical period, Architectural Modernism as an artistic style which is a product of this paradigm and this historical period. In this film, dialectics of Enlightment/mitology and Architectural Modernism/historical content entwined. In reality, the tension between utopian futuristic architecture based on machine aesthetics of Metropolis and its distopian techno-totaliterian social order reflected the tension between utopian characteristic of Modern Avant-garde in architecture who rejects to use historical styles and historical content as mitology

Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.

The QT interval, an electrocardiographic measure reflecting myocardial repolarization, is a heritable trait. QT prolongation is a risk factor for ventricular arrhythmias and sudden cardiac death (SCD) and could indicate the presence of the potentially lethal mendelian long-QT syndrome (LQTS). Using a genome-wide association and replication study in up to 100,000 individuals, we identified 35 common variant loci associated with QT interval that collectively explain ∼8-10% of QT-interval variation and highlight the importance of calcium regulation in myocardial repolarization. Rare variant analysis of 6 new QT interval-associated loci in 298 unrelated probands with LQTS identified coding variants not found in controls but of uncertain causality and therefore requiring validation. Several newly identified loci encode proteins that physically interact with other recognized repolarization proteins. Our integration of common variant association, expression and orthogonal protein-protein interaction screens provides new insights into cardiac electrophysiology and identifies new candidate genes for ventricular arrhythmias, LQTS and SCD

Structure-function analysis of the <em>Fusarium oxysporum</em> Avr2 effector allows uncoupling of its immune-suppressing activity from recognition

Plant pathogens employ effector proteins to manipulate their hosts. Fusarium oxysporum f. sp. lycopersici (Fol), the causal agent of tomato wilt disease, produces effector protein Avr2. Besides being a virulence factor, Avr2 triggers immunity in I-2 carrying tomato (Solanum lycopersicum). Fol strains that evade I-2 recognition carry point mutations in Avr2 (e.g. Avr2R45H), but retain full virulence. Here we investigate the virulence function of Avr2 and determine its crystal structure. Transgenic tomato and Arabidopsis expressing either wild-type ΔspAvr2 (deleted signal-peptide) or the ΔspAvr2R45H variant become hypersusceptible to fungal, and even bacterial infections, suggesting that Avr2 targets a conserved defense mechanism. Indeed, Avr2 transgenic plants are attenuated in immunity-related readouts, including flg22-induced growth inhibition, ROS production and callose deposition. The crystal structure of Avr2 reveals that the protein shares intriguing structural similarity to ToxA from the wheat pathogen Pyrenophora tritici-repentis and to TRAF proteins. The I-2 resistance-breaking Avr2V41M, Avr2R45H and Avr2R46P variants cluster on a surface-presented loop. Structure-guided mutagenesis enabled uncoupling of virulence from I-2-mediated recognition. We conclude that I-2-mediated recognition is not based on monitoring Avr2 virulence activity, which includes suppression of immune responses via an evolutionarily conserved effector target, but by recognition of a distinct epitope

The Merits of Playing It by the Book: Routine versus Deliberate Learning and the Development of Dynamic Capabilities

In this study, we investigate the nature of dynamic capabilities and use a fine-grained measurement to test how centralization, routinization, and formalization relate to the underlying learning components of dynamic capabilities. We find that the effects of our three dimensions of managerial practices are broadly similar for almost all components of dynamic capabilities, and that only a few show a different pattern. Centralization and routinization are negatively related to dynamic capabilities, formalization is shown to have a significantly positive effect. We provide insights into the role of three dimensions of managerial practice by explaining variation among the learning components of dynamic capabilities. This has implications for the nature and development of dynamic capabilities as well as for the routine versus deliberate learning debate