Collectively, we found that all of variant RARA rearrangements shared some similar aspects with PML-RARA in molecular biology. First, the ability of forming homodimers or heretodimers with RXRA; Second, the recruitment of corepressors; Third, the dominate negative role on the RARA-transcriptional program. Though differences existed in the partners of RARA rearrangments and detailed functions of distinct fusions, these aspects determined to generate the similar phenotype of APL. However, variant RARA rearrangements lacked the target for ATO, while only a part of them was sensitive to ATRA-mediated differentiation induction and degradation. Therefore, it brought more difficulties to treat variant APL than typical APL (Fig. 2a).

Retinoids, i.e., natural and synthetic vitamin A derivatives, have been studied for decades in clinical trials due to their established role in regulating cell growth, differentiation and apoptosis. Retinoids are key compounds in biological differentiation therapy. Retinoids have critical functions in many aspects of human biology: at the cellular level, they control cell differentiation, growth, and apoptosis [3]. Several biologically active vitamin A derivatives, namely, all-trans retinoic acid (ATRA), 9-cis retinoic acid (9-cis-RA), and 13-cis retinoic acid (13-cis-RA), have been tested for potential use in cancer therapy and chemoprevention [4,5,6,7]. The most effective clinical use of ATRA was demonstrated in acute promyelocytic leukemia (APL) treatment [8]. Additional studies have indicated that 13-cis-RA is beneficial in high-risk neuroblastoma (NBL) treatment after bone marrow transplantation, suggesting that retinoids may play an adjuvant therapeutic role in the management of minimal residual disease [9]. List of all human malignancies, for which the clinical treatment with retinoids was already tested, is given in the Table 1.


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Regarding CRC biology, FOXM1 expression levels have been reported to be correlated with cancer progression, lymph node and liver metastasis and high TNM stages [124,125,126,127]. These findings agreed with decreased patient survival rate. Interestingly, high concurrent FOXM1 and CAV-1 (caveolin 1) overexpression plays an important role in CRC development and progression by negatively regulating E-cadherin [128].

Regarding miRNA mechanisms leading to FOXM1 knock-down, it has been shown that the downregulation of miR-320, miR-149, mi-R-342 is related to CRC biology [140,141,142,143,144]. Notably, miR-320 and miR-342 are suppressors of both FOXM1 and FOXQ1, constituting potentially interesting therapeutic tools for CRC [143, 144]. Clinically, FOXM1 may be used directly as a diagnostic/prognostic marker as high expression levels have been correlated, in independent cohorts of CRC patients, with poor survival [144]. In addition, due to its clear oncogenic nature FOXM1 has emerged as promissory target for cancer drug therapy [145].

The developed model consists of directionally-tuned neurons, shown to exist in M1 in biology, that encode the hand position through average neural firing. The force field is modeled through a simulated, external current perturbing the neural activity in the direction of the force field. In biology, Norepinephrine is released from locus coreuleus to M1 when errors are detected in the visual pathway. Norepinephrine affects M1 in a goal-directed manner, increasing the excitatory synaptic responses in the so-called hotspot, which is determined by arousal. For the model to remain close to biology, adaptation is modeled through an error-dependent increase in excitatory to excitatory conductance in the target position within the M1 model, leading to a decrease of the perturbation on the stable bump of neural activity across trials. Washout is implemented through a shift of the hotspot and the accumulated Norepinephrine through a motor-coordinate system shift during force field removal. After the initial washout trial, the wrongful coordinate system shift is detected and Norepinephrine in the shifted hotspot decays.

Inspired by synaptic competition in biology, we have come up with a simple and local gradient descent optimization algorithm that can reduce training time, with no demand on past information. Our algorithm works similarly to the traditional gradient descent used in back-propagation, except that instead of having a uniform learning rate across all synapses, the learning rate depends on the current connection weights of individual synapses and the L2norm of the weights of each neuron.

NetPyNE is a Python interface to NEURON which addresses these issues. It features a user-friendly, high-level declarative programming language. At the network level for example, NetPyNE automatically generates connectivity using a concise set of user-defined specifications rather than forcing the user to explicitly define millions of cell-to-cell connections. NetPyNE enables users to generate NEURON models, run them efficiently in automatically parallelized simulations, optimize and explore network parameters through automated batch runs, and use built-in functions for a wide variety of visualizations and analyses. NetPyNE facilitates sharing by exporting and importing standardized formats (NeuroML and SONATA), and is being widely used to investigate different brain phenomena. It is also being used to teach basic neurobiology and neural modeling. NetPyNE has recently added support for CoreNEURON, the compute engine of NEURON optimized for the latest supercomputer hardware architectures.

Nixon RA, Paskevich PA, Sihag RK, Thayer CY. Phosphorylation on carboxyl terminus domains of neurofilament proteins in retinal ganglion cell neurons in vivo: influences on regional neurofilament accumulation, interneurofilament spacing, and axon caliber. The Journal of cell biology. 1994; 126(4): 1031-46.

Cal C, et al. 3D cellular reconstruction of cortical glia and parenchymal morphometric analysis from Serial Block-Face Electron Microscopy of juvenile rat. Progress in Neurobiology. 2019;183: 101696.

Curation and knowledge dissemination of the computational neuroscience field requires many unique considerations as it utilizes language, methods, and ideas from diverse areas including biology, chemistry, physics, mathematics, medicine, and computer science. In order to effectively facilitate curation and knowledge dissemination for the computational neuroscience community we must first develop a robust representation of its existing literature. Using unsupervised topic modeling approaches, a metadata tagging schema was developed for computational neuroscience literature from ModelDB (a repository of computational neuroscience models), and compared to that of a larger neuroscience corpus. This analysis shows key differences in the types of discoveries and knowledge addressed in neuroscience and its computational subdiscipline, and gives insight into how an automated question answering system might differ between the two. be457b7860

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