Label-Dependencies Aware Recurrent Neural Networks

In the last few years, Recurrent Neural Networks (RNNs) have proved effective on several NLP tasks. Despite such great success, their ability to model \emph{sequence labeling} is still limited. This lead research toward solutions where RNNs are combined with models which already proved effective in this domain, such as CRFs. In this work we propose a solution far simpler but very effective: an evolution of the simple Jordan RNN, where labels are re-injected as input into the network, and converted into embeddings, in the same way as words. We compare this RNN variant to all the other RNN models, Elman and Jordan RNN, LSTM and GRU, on two well-known tasks of Spoken Language Understanding (SLU). Thanks to label embeddings and their combination at the hidden layer, the proposed variant, which uses more parameters than Elman and Jordan RNNs, but far fewer than LSTM and GRU, is more effective than other RNNs, but also outperforms sophisticated CRF models.Comment: 22 pages, 3 figures. Accepted at CICling 2017 conference. Best Verifiability, Reproducibility, and Working Description awar

Small inhibitor of Bcl-2, HA14-1, selectively enhanced the apoptotic effect of cisplatin by modulating Bcl-2 family members in MDA-MB-231 breast cancer cells

Inhibition or downregulation of Bcl-2 represents a new therapeutic approach to by-pass chemoresistance in cancer cells. Therefore, we explored the potential of this approach in breast cancer cells. Cisplatin and paclitaxel induced apoptosis in a dose-dependent manner in MCF-7 (drug-sensitive) and MDA-MB-231 (drug-insensitive) cells. Furthermore, when we transiently silenced Bcl-2, both cisplatin and paclitaxel induced apoptosis more than parental cells. Dose dependent induction of apoptosis by drugs was enhanced by the pre-treatment of these cells with HA14-1, a Bcl-2 inhibitor. Although the effect of cisplatin was significant on both cell lines, the effect of paclitaxel was much less potent only in MDA-MB-231 cells. To further understand the distinct role of drugs in MDA-MB-231 cells pretreated with HA14-1, caspases and Bcl-2 family proteins were studied. The apoptotic effect of cisplatin with or without HA14-1 pre-treatment is shown to be caspase-dependent. Among pro-apoptotic Bcl-2 proteins, Bax and Puma were found to be up-regulated whereas Bcl-2 and Bcl-x(L) were down-regulated when cells were pretreated with HA14-1 followed by paclitaxel or cisplatin. Enforced Bcl-2 expression in MDA-MB-231 cells abrogated the sensitizing effect of HA14-1 in cisplatin induced apoptosis. These results suggest that the potentiating effect of HA14-1 is drug and cell type specific and may not only depend on the inhibition of Bcl-2. Importantly, alteration of other pro-apoptotic or anti-apoptotic Bcl-2 family members may dictate the apoptotic response when HA14-1 is combined with chemotherapeutic drugs

CubeNet: Equivariance to 3D Rotation and Translation

3D Convolutional Neural Networks are sensitive to transformations applied to their input. This is a problem because a voxelized version of a 3D object, and its rotated clone, will look unrelated to each other after passing through to the last layer of a network. Instead, an idealized model would preserve a meaningful representation of the voxelized object, while explaining the pose-difference between the two inputs. An equivariant representation vector has two components: the invariant identity part, and a discernable encoding of the transformation. Models that can't explain pose-differences risk "diluting" the representation, in pursuit of optimizing a classification or regression loss function. We introduce a Group Convolutional Neural Network with linear equivariance to translations and right angle rotations in three dimensions. We call this network CubeNet, reflecting its cube-like symmetry. By construction, this network helps preserve a 3D shape's global and local signature, as it is transformed through successive layers. We apply this network to a variety of 3D inference problems, achieving state-of-the-art on the ModelNet10 classification challenge, and comparable performance on the ISBI 2012 Connectome Segmentation Benchmark. To the best of our knowledge, this is the first 3D rotation equivariant CNN for voxel representations.Comment: Preprin

Therapeutic Radionuclides: Making the Right Choice

Recently, there has been a resurgence of interest in nuclear medicine therapeutic procedures. Using unsealed sources for therapy is not a new concept; it has been around since the beginnings of nuclear medicine. Treatment of thyroid disorders with radioiodine is a classic example. The availability of radionuclides with suitable therapeutic properties for specific applications, as well as methods for their selective targeting to diseased tissue have, however, remained the main obstacles for therapy to assume a more widespread role in nuclear medicine. Nonetheless, a number of new techniques that have recently emerged, (e.g., tumor therapy with radiolabeled monoclonal antibodies, treatment of metastatic bone pain, etc.) appear to have provided a substantial impetus to research on production of new therapeutic radionuclides. Although there are a number of new therapeutic approaches requiring specific radionuclides, only selected broad areas will be used as examples in this article

Ant-based Neural Topology Search (ANTS) for Optimizing Recurrent Networks

Hand-crafting effective and efficient structures for recurrent neural networks (RNNs) is a difficult, expensive, and time-consuming process. To address this challenge, we propose a novel neuro-evolution algorithm based on ant colony optimization (ACO), called Ant-based Neural Topology Search (ANTS), for directly optimizing RNN topologies. The procedure selects from multiple modern recurrent cell types such as ∆-RNN, GRU, LSTM, MGU and UGRNN cells, as well as recurrent connections which may span multiple layers and/or steps of time. In order to introduce an inductive bias that encourages the formation of sparser synaptic connectivity patterns, we investigate several variations of the core algorithm. We do so primarily by formulating different functions that drive the underlying pheromone simulation process (which mimic L1 and L2 regularization in standard machine learning) as well as by introducing ant agents with specialized roles (inspired by how real ant colonies operate), i.e., explorer ants that construct the initial feed forward structure and social ants which select nodes from the feed forward connections to subsequently craft recurrent memory structures. We also incorporate communal intelligence, where best weights are shared by the ant colony for weight initialization, reducing the number of backpropagation epochs required to locally train candidate RNNs, speeding up the neuro-evolution process. Our results demonstrate that the sparser RNNs evolved by ANTS significantly outperform traditional one and two layer architectures consisting of modern memory cells, as well as the well-known NEAT algorithm. Furthermore, we improve upon prior state-of-the-art results on the time series dataset utilized in our experiments

Endovascular covered stenting for the management of post-percutaneous nephrolithotomy renal pseudoaneurysm: a case report

<p>Abstract</p> <p>Introduction</p> <p>Intrarenal pseudoaneurysm is a rare, yet clinically significant, complication of percutaneous nephrolithotomy. A high index of clinical suspicion is necessary in order to recognize pseudoaneurysm as the cause of delayed bleeding after percutaneous nephrolithotomy and angiography confirms the diagnosis which allows endovascular management.</p> <p>Case presentation</p> <p>We present a case of a 65-year old Caucasian woman who underwent percutaneous nephrolithotomy in the supine position for a two centimetre renal calculus. The postoperative course was complicated by persistent bleeding due to a renal pseudoaneurysm. The vascular lesion was successfully managed by endovascular exclusion through the use of a covered stent graft. We report the first successful use of this method for the management of iatrogenic pseudoaneurysm in a branch of the left renal artery and we focus on the imaging findings, technical details, advantages and limitations of this technique.</p> <p>Conclusion</p> <p>As a result of its high efficacy, interventional radiology has largely replaced open surgery for the management of renal pseudoaneurysm related to percutaneous nephrolithotomy. Recent technical advancements have allowed the use of covered stent grafts as an alternative to embolisation for the angiographic management of visceral artery pseudoaneurysm located in other organs. This novel technique allows the endovascular exclusion of the pseudoaneurysm, without compromising arterial supply to the end-structures - an advantage of critical importance in organs supplied by segmental arteries - in the absence of collateral vasculature, such as the kidney.</p

Cross-protection against European swine influenza viruses in the context of infection immunity against the 2009 pandemic H1N1 virus : studies in the pig model of influenza

Pigs are natural hosts for the same influenza virus subtypes as humans and are a valuable model for cross-protection studies with influenza. In this study, we have used the pig model to examine the extent of virological protection between a) the 2009 pandemic H1N1 (pH1N1) virus and three different European H1 swine influenza virus (SIV) lineages, and b) these H1 viruses and a European H3N2 SIV. Pigs were inoculated intranasally with representative strains of each virus lineage with 6- and 17-week intervals between H1 inoculations and between H1 and H3 inoculations, respectively. Virus titers in nasal swabs and/or tissues of the respiratory tract were determined after each inoculation. There was substantial though differing cross-protection between pH1N1 and other H1 viruses, which was directly correlated with the relatedness in the viral hemagglutinin (HA) and neuraminidase (NA) proteins. Cross-protection against H3N2 was almost complete in pigs with immunity against H1N2, but was weak in H1N1/pH1N1-immune pigs. In conclusion, infection with a live, wild type influenza virus may offer substantial cross-lineage protection against viruses of the same HA and/or NA subtype. True heterosubtypic protection, in contrast, appears to be minimal in natural influenza virus hosts. We discuss our findings in the light of the zoonotic and pandemic risks of SIVs

Overexpression of cathepsin K in mice decreases collagen deposition and lung resistance in response to bleomycin-induced pulmonary fibrosis

<p>Abstract</p> <p>Background</p> <p>Lung fibrosis is a devastating pulmonary disorder characterized by alveolar epithelial injury, extracellular matrix deposition and scar tissue formation. Due to its potent collagenolytic activity, cathepsin K, a lysosomal cysteine protease is an interesting target molecule with therapeutic potential to attenuate bleomycin-induced pulmonary fibrosis in mice. We here tested the hypothesis that over-expression of cathepsin K in the lungs of mice is protective in bleomycin-induced pulmonary fibrosis.</p> <p>Methods</p> <p>Wild-type and cathepsin K overexpressing (cathepsin K transgenic; cath K tg) mice were challenged intratracheally with bleomycin and sacrificed at 1, 2, 3 and 4 weeks post-treatment followed by determination of lung fibrosis by estimating lung collagen content, lung histopathology, leukocytic infiltrates and lung function. In addition, changes in cathepsin K protein levels in the lung were determined by immunohistochemistry, real time RT-PCR and western blotting.</p> <p>Results</p> <p>Cathepsin K protein levels were strongly increased in alveolar macrophages and lung parenchymal tissue of mock-treated cathepsin K transgenic (cath K tg) mice relative to wild-type mice and further increased particularly in cath K tg but also wild-type mice in response to bleomycin. Moreover, cath K tg mice responded with a lower collagen deposition in their lungs, which was accompanied by a significantly lower lung resistance (R_L) compared to bleomycin-treated wild-type mice. In addition, cath K tg mice responded with a lower degree of lung fibrosis than wild-type mice, a process that was found to be independent of inflammatory leukocyte mobilization in response to bleomycin challenge.</p> <p>Conclusion</p> <p>Over-expression of cathepsin K reduced lung collagen deposition and improved lung function parameters in the lungs of transgenic mice, thereby providing at least partial protection against bleomycin-induced lung fibrosis.</p