Evaluating surgical skills from kinematic data using convolutional neural networks

The need for automatic surgical skills assessment is increasing, especially because manual feedback from senior surgeons observing junior surgeons is prone to subjectivity and time consuming. Thus, automating surgical skills evaluation is a very important step towards improving surgical practice. In this paper, we designed a Convolutional Neural Network (CNN) to evaluate surgeon skills by extracting patterns in the surgeon motions performed in robotic surgery. The proposed method is validated on the JIGSAWS dataset and achieved very competitive results with 100% accuracy on the suturing and needle passing tasks. While we leveraged from the CNNs efficiency, we also managed to mitigate its black-box effect using class activation map. This feature allows our method to automatically highlight which parts of the surgical task influenced the skill prediction and can be used to explain the classification and to provide personalized feedback to the trainee.Comment: Accepted at MICCAI 201

De novo protein design:How do we expand into the universe of possible protein structures?

Protein scientists are paving the way to a new phase in protein design and engineering. Approaches and methods are being developed that could allow the design of proteins beyond the confines of natural protein structures. This possibility of designing entirely new proteins opens new questions: What do we build? How do we build into protein-structure space where there are few, if any, natural structures to guide us? To what uses can the resulting proteins be put? And, what, if anything, does this pursuit tell us about how natural proteins fold, function and evolve? We describe the origins of this emerging area of fully de novo protein design, how it could be developed, where it might lead, and what challenges lie ahead

Conformational Dynamics of Asparagine at Coiled-Coil Interfaces

Coiled coils (CCs) are among the best-understood protein folds. Nonetheless, there are gaps in our knowledge of CCs. Notably, CCs are likely to be structurally more dynamic than often considered. Here, we explore this in an abundant class of CCs, parallel dimers, focusing on polar asparagine (Asn) residues in the hydrophobic interface. It is well documented that such inclusions discriminate between different CC oligomers, which has been rationalized in terms of whether the Asn can make side-chain hydrogen bonds. Analysis of parallel CC dimers in the Protein Data Bank reveals a variety of Asn side-chain conformations, but not all of these make the expected inter-side-chain hydrogen bond. We probe the structure and dynamics of a <i>de novo</i>-designed coiled-coil homodimer, CC-Di, by multidimensional nuclear magnetic resonance spectroscopy, including model-free dynamical analysis and relaxation–dispersion experiments. We find dynamic exchange on the millisecond time scale between Asn conformers with the side chains pointing into and out of the core. We perform molecular dynamics simulations that are consistent with this, revealing that the side chains are highly dynamic, exchanging between hydrogen-bonded-paired conformations in picoseconds to nanoseconds. Combined, our data present a more dynamic view for Asn at CC interfaces. Although inter-side-chain hydrogen bonding states are the most abundant, Asn is not always buried or engaged in such interactions. Because interfacial Asn residues are key design features for modulating CC stability and recognition, these further insights into how they are accommodated within CC structures will aid their predictive modeling, engineering, and design

Anaplastic carcinoma of the pancreas producing granulocyte-colony stimulating factor: a case report

<p>Abstract</p> <p>Introduction</p> <p>The granulocyte-colony stimulating factor-producing tumor was first reported in 1977, however, anaplastic pleomorphic type carcinoma of the pancreas producing granulocyte-colony stimulating factor is still rare.</p> <p>Case presentation</p> <p>A 63-year-old man was admitted to our hospital with body weight loss (-10 kg during months) and upper abdominal pain from 3 weeks. Abdominal computed tomography demonstrated a pancreatic tumor 10 cm in size and multiple low-density areas in the liver. On admission, the peripheral leukocyte count was elevated to 91,500/mm³and the serum concentration of granulocyte-colony stimulating factor was 134 pg/mL (normal, < 18.1 pg/mL). Based on liver biopsy findings, the tumor was classified as an anaplastic pleomorphic-type carcinoma. Immunohistochemical staining showed that pancreatic carcinoma cells were positive for granulocyte-colony stimulating factor. The patient developed interstitial pneumonia, probably caused by granulocyte-colony stimulating factor, and died 11 days after admission.</p> <p>Conclusion</p> <p>This is a rare case report of anaplastic pleomorphic-type carcinoma of the pancreas producing granulocyte-colony stimulating factor and confirmed by immunohistochemistry.</p

Membrane-spanning α-helical barrels as tractable protein-design targets

The rational (de novo) design of membrane-spanning proteins lags behind that for water-soluble globular proteins. This is due to gaps in our knowledge of membrane-protein structure, and experimental difficulties in studying such proteins compared to water-soluble counterparts. One limiting factor is the small number of experimentally determined three-dimensional structures for transmembrane proteins. By contrast, many tens of thousands of globular protein structures provide a rich source of ‘scaffolds’ for protein design, and the means to garner sequence-to-structure relationships to guide the design process. The α-helical coiled coil is a protein-structure element found in both globular and membrane proteins, where it cements a variety of helix–helix interactions and helical bundles. Our deep understanding of coiled coils has enabled a large number of successful de novo designs. For one class, the α-helical barrels—that is, symmetric bundles of five or more helices with central accessible channels—there are both water-soluble and membrane-spanning examples. Recent computational designs of water-soluble α-helical barrels with five to seven helices have advanced the design field considerably. Here we identify and classify analogous and more complicated membrane-spanning α-helical barrels from the Protein Data Bank. These provide tantalizing but tractable targets for protein engineering and de novo protein design

R-CHOP versus R-CVP in the treatment of follicular lymphoma: a meta-analysis and critical appraisal of current literature

which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Purpose: R-CHOP (rituximab with cyclophosphamide, doxorubicin, vincristine and prednisone) and R-CVP (rituximab with cyclophosphamide, vincristine and prednisone) have both been used successfully in the treatment of patients with symptomatic follicular lymphoma (FL). No study has compared the efficacy of the two treatment modalities and attempted to evaluate the role of anthracyclines in the management of patients with FL. We conducted a meta-analysis of relevant literature comparing the two treatment arms for FL with response being the final endpoint. Patients and Methods: Two analyses were conducted: The first analysis compared R-CHOP to R-CVP as frontline agents for the treatment of FL, and the second analysis included both untreated and relapsed patients. Results: For both studies, R-CVP was superior to R-CHOP when evaluating for complete response (CR). Odds ratios were 2.86 (95 % CI, 1.81–4.51) in the first analysis and 1.48 (95 % CI, 0.991–2.22) in the second analysis. However for overall response (CR+Partial response, PR), R-CHOP was superior, with odds ratios of 5.45 (95 % CI: 2.51 – 11.83) and 5.54 (95 % CI: 2.69

Japanese epidemiological survey with consensus statement on Japanese guidelines for treatment of iron overload in bone marrow failure syndromes

Many patients with bone marrow failure syndromes need frequent transfusions of red blood cells, and most of them eventually suffer from organ dysfunction induced by excessively accumulated iron. The only way to treat transfusion-induced iron overload is iron chelating therapy. However, most patients have not been treated effectively because daily/continuous administration of deferoxamine is difficult for outpatients. Recently, a novel oral iron chelator, deferasirox, has been developed, and introduction of the drug may help many patients benefit from iron chelation therapy. In this review, we will discuss the current status of iron overload in transfusion-dependent patients, and the development of Japanese guidelines for the treatment of iron overload in Japan, which were established by the National Research Group on Idiopathic Bone Marrow Failure Syndromes in Japan