Objective comparison of methods to decode anomalous diffusion

Deviations from Brownian motion leading to anomalous diffusion are found in transport dynamics from quantum physics to life sciences. The characterization of anomalous diffusion from the measurement of an individual trajectory is a challenging task, which traditionally relies on calculating the trajectory mean squared displacement. However, this approach breaks down for cases of practical interest, e.g., short or noisy trajectories, heterogeneous behaviour, or non-ergodic processes. Recently, several new approaches have been proposed, mostly building on the ongoing machine-learning revolution. To perform an objective comparison of methods, we gathered the community and organized an open competition, the Anomalous Diffusion challenge (AnDi). Participating teams applied their algorithms to a commonly-defined dataset including diverse conditions. Although no single method performed best across all scenarios, machine-learning-based approaches achieved superior performance for all tasks. The discussion of the challenge results provides practical advice for users and a benchmark for developers

New insights into the synergism of nucleoside analogs with radiotherapy

Nucleoside analogs have been frequently used in combination with radiotherapy in the clinical setting, as it has long been understood that inhibition of DNA repair pathways is an important means by which many nucleoside analogs synergize. Recent advances in our understanding of the structure and function of deoxycytidine kinase (dCK), a critical enzyme required for the anti-tumor activity for many nucleoside analogs, have clarified the mechanistic role this kinase plays in chemo- and radio-sensitization. A heretofore unrecognized role of dCK in the DNA damage response and cell cycle machinery has helped explain the synergistic effect of these agents with radiotherapy. Since most currently employed nucleoside analogs are primarily activated by dCK, these findings lend fresh impetus to efforts focused on profiling and modulating dCK expression and activity in tumors. In this review we will briefly review the pharmacology and biochemistry of the major nucleoside analogs in clinical use that are activated by dCK. This will be followed by discussions of recent advances in our understanding of dCK activation via post-translational modifications in response to radiation and current strategies aimed at enhancing this activity in cancer cells

Medical students’ creative projects on a third year pediatrics clerkship: a qualitative analysis of patient-centeredness and emotional connection

BACKGROUND: Increasingly, medical educators are incorporating reflective writing and original creative work into educational practices with the goals of stimulating student self-awareness, appreciation of multiple perspectives, and comfort with ambiguity and uncertainty. This study investigated students’ creative projects to assess the extent to which they adopted a patient/relationship-centered, emotionally connected position toward patients and families. METHODS: Over a 10 year period, students on a required third year pediatrics clerkship individually or in groups completed either a reflection or an education project using a creative medium. 520 projects (representing 595 students, 74.7 % of total eligible students) were qualitatively analyzed according to various thematic and emotion-based dimensions. RESULTS: The majority of projects were personal narrative essays and poetry. The largest number of project themes related to the importance of patient/relationship-centered medicine with patients. The next largest number of projects focused on health education of parents, patients, or classmates. In telling their stories, students were more likely to use a personal voice representing either their or the patient’s perspective than an objective, impersonal one. In terms of emotional tone, projects were more likely to be serious than humorous. The largest number of students’ emotions expressed an empathic tone. Students identified a large number and wide range of both negative and positive feelings in themselves and their patients. The majority of student emotions were positive, while the majority of patient and family emotions were negative. CONCLUSIONS: Students’ preference for patient-centered, relational themes, as well as their tendency to favor the first voice, empathic tone, and willingness to express a range of positive and negative emotions in presenting their projects, suggests that they valued emotional connection with patients and families during the pediatrics clerkship experience

Dynamic coronary roadmapping via catheter tip tracking in X-ray fluoroscopy with deep learning based Bayesian filtering

Percutaneous coronary intervention (PCI) is typically performed with image guidance using X-ray angiograms in which coronary arteries are opacified with X-ray opaque contrast agents. Interventional cardiologists typically navigate instruments using non-contrast-enhanced fluoroscopic images, since higher use of contrast agents increases the risk of kidney failure. When using fluoroscopic images, the interventional cardiologist needs to rely on a mental anatomical reconstruction. This paper reports on the development of a novel dynamic coronary roadmapping approach for improving visual feedback and reducing contrast use during PCI. The approach compensates cardiac and respiratory induced vessel motion by ECG alignment and catheter tip tracking in X-ray fluoroscopy, respectively. In particular, for accurate and robust tracking of the catheter tip, we proposed a new deep learning based Bayesian filtering method that integrates the detection outcome of a convolutional neural network and the motion estimation between frames using a particle filtering framework. The proposed roadmapping and tracking approaches were validated on clinical X-ray images, achieving accurate performance on both catheter tip tracking and dynamic coronary roadmapping experiments. In addition, our approach runs in real-time on a computer with a single GPU and has the potential to be integrated into the clinical workflow of PCI procedures, providing cardiologists with visual guidance during interventions without the need of extra use of contrast agent.Accepted Author ManuscriptOptical and Laser Remote Sensin

Deoxycytidine kinase regulates the G2/M checkpoint through interaction with cyclin-dependent kinase 1 in response to DNA damage.

Deoxycytidine kinase (dCK) is a rate limiting enzyme critical for phosphorylation of endogenous deoxynucleosides for DNA synthesis and exogenous nucleoside analogues for anticancer and antiviral drug actions. dCK is activated in response to DNA damage; however, how it functions in the DNA damage response is largely unknown. Here, we report that dCK is required for the G2/M checkpoint in response to DNA damage induced by ionizing radiation (IR). We demonstrate that the ataxia-telangiectasia-mutated (ATM) kinase phosphorylates dCK on Serine 74 to activate it in response to DNA damage. We further demonstrate that Serine 74 phosphorylation is required for initiation of the G2/M checkpoint. Using mass spectrometry, we identified a protein complex associated with dCK in response to DNA damage. We demonstrate that dCK interacts with cyclin-dependent kinase 1 (Cdk1) after IR and that the interaction inhibits Cdk1 activity both in vitro and in vivo. Together, our results highlight the novel function of dCK and provide molecular insights into the G2/M checkpoint regulation in response to DNA damage