Combining reinforcement learning (RL) and molecular dynamics (MD) simulations, we propose a machine-learning approach, called RL
‡
, to automatically unravel chemical reaction mechanisms. In RL
‡
, ...locating the transition state of a chemical reaction is formulated as a game, and two functions are optimized, one for value estimation and the other for policy making, to iteratively improve our chance of winning this game. Both functions can be approximated by deep neural networks. By virtue of RL
‡
, one can directly interpret the reaction mechanism according to the value function. Meanwhile, the policy function allows efficient sampling of the transition path ensemble, which can be further used to analyze reaction dynamics and kinetics. Through multiple experiments, we show that RL
‡
can be trained
tabula rasa
hence allowing us to reveal chemical reaction mechanisms with minimal subjective biases.
RL
‡
can automatically locate the transition states of chemical reactions through deep reinforcement learning of feedback from molecular simulations.
In order to efficiently overcome high free energy barriers embedded in a complex energy landscape and calculate overall thermodynamics properties using molecular dynamics simulations, we developed ...and implemented a sampling strategy by combining the metadynamics with (selective) integrated tempering sampling (ITS/SITS) method. The dominant local minima on the potential energy surface (PES) are partially exalted by accumulating history-dependent potentials as in metadynamics, and the sampling over the entire PES is further enhanced by ITS/SITS. With this hybrid method, the simulated system can be rapidly driven across the dominant barrier along selected collective coordinates. Then, ITS/SITS ensures a fast convergence of the sampling over the entire PES and an efficient calculation of the overall thermodynamic properties of the simulation system. To test the accuracy and efficiency of this method, we first benchmarked this method in the calculation of ϕ - ψ distribution of alanine dipeptide in explicit solvent. We further applied it to examine the design of template molecules for aromatic meta-C-H activation in solutions and investigate solution conformations of the nonapeptide Bradykinin involving slow cis-trans isomerizations of three proline residues.
High potential energy barriers and engagement of solvent coordinates set challenges for in silico studies of chemical reactions, and one is quite commonly limited to study reactions along predefined ...reaction coordinate(s). A systematic protocol, QM/MM MD simulations using enhanced sampling of reactive trajectories (ESoRT), is established to quantitatively study chemical transitions in complex systems. A number of trajectories for Claisen rearrangement in water and toluene were collected and analyzed, respectively. Evidence was found that the bond making and breaking during this reaction are concerted processes in solutions, preferentially through a chairlike configuration. Water plays an important dynamic role that helps stabilize the transition sate, and the dipole–dipole interaction between water and the solute also lowers the transition barrier. The calculated rate coefficient is consistent with the experimental measurement. Compared with water, the reaction pathway in toluene is “narrower” and the reaction rate is slower by almost three orders of magnitude due to the absence of proper interactions to stabilize the transition state. This study suggests that the “in-water” nature of the Claisen rearrangement in aqueous solution influences its thermodynamics, kinetics, as well as dynamics.
Analysis of extracellular vesicles (EVs) derived from plasma or cerebrospinal fluid (CSF) has emerged as a promising biomarker platform for therapeutic monitoring in glioblastoma patients. However, ...the contents of the various subpopulations of EVs in these clinical specimens remain poorly defined. Here we characterize the relative abundance of miRNA species in EVs derived from the serum and cerebrospinal fluid of glioblastoma patients. EVs were isolated from glioblastoma cell lines as well as the plasma and CSF of glioblastoma patients. The microvesicle subpopulation was isolated by pelleting at 10,000×
g
for 30 min after cellular debris was cleared by a 2000×
g
(20 min) spin. The exosome subpopulation was isolated by pelleting the microvesicle supernatant at 120,000×
g
(120 min). qRT-PCR was performed to examine the distribution of miR-21, miR-103, miR-24, and miR-125. Global miRNA profiling was performed in select glioblastoma CSF samples. In plasma and cell line derived EVs, the relative abundance of miRNAs in exosome and microvesicles were highly variable. In some specimens, the majority of the miRNA species were found in exosomes while in other, they were found in microvesicles. In contrast, CSF exosomes were enriched for miRNAs relative to CSF microvesicles. In CSF, there is an average of one molecule of miRNA per 150–25,000 EVs. Most EVs derived from clinical biofluids are devoid of miRNA content. The relative distribution of miRNA species in plasma exosomes or microvesicles is unpredictable. In contrast, CSF exosomes are the major EV compartment that harbor miRNAs.
Abstract
BACKGROUND
Vestibular schwannomas (VS) are benign tumors derived from Schwann cells ensheathing the vestibulocochlear nerve. The retrosigmoid (RS) surgical approach is useful to resect ...tumors of multiple sizes while affording the possibility of preserving postoperative hearing.
OBJECTIVE
To conduct a systematic review of published literature investigating hearing preservation rates in patients who underwent the RS approach for VS treatment.
METHODS
The PubMed, Scopus, and Embase databases were surveyed for studies that reported preoperative and postoperative hearing grades on VS patients who underwent RS treatment. Hearing preservation rates were calculated, and additional patient demographic data were extracted. Tumor size data were stratified to compare hearing preservation rates after surgery for intracanalicular, small (0-20 mm), and large (>20 mm) tumors.
RESULTS
Of 383 deduplicated articles, 26 studies (6.8%) met eligibility criteria for a total of 2034 patients with serviceable preoperative hearing, for whom postoperative hearing status was evaluated. Aggregate hearing preservation was 31% and 35% under a fixed and random effects model, respectively. A mixed effects model was used to determine hearing preservation rates depending on tumor size, which were determined to be 57%, 37%, and 12% for intracanalicular, small, and large tumors, respectively. Significant cross-study heterogeneity was found (I2 = 93%, τ2 = .964, P < .01; Q = 287.80, P = < .001), with rates of hearing preservation ranging from 0% to 100%.
CONCLUSION
Tumor size may have an effect on hearing preservation rates, but multiple factors should be considered. Discussion of a patient's expectations for hearing preservation is critical when deciding on VS treatment plans.
RNAs within extracellular vesicles (EVs) have potential as diagnostic biomarkers for patients with cancer and are identified in a variety of biofluids. Glioblastomas (GBMs) release EVs containing RNA ...into cerebrospinal fluid (CSF). Here we describe a multi-institutional study of RNA extracted from CSF-derived EVs of GBM patients to detect the presence of tumor-associated amplifications and mutations in epidermal growth factor receptor (EGFR).
CSF and matching tumor tissue were obtained from patients undergoing resection of GBMs. We determined wild-type (wt)EGFR DNA copy number amplification, as well as wtEGFR and EGFR variant (v)III RNA expression in tumor samples. We also characterized wtEGFR and EGFRvIII RNA expression in CSF-derived EVs.
EGFRvIII-positive tumors had significantly greater wtEGFR DNA amplification (P = 0.02) and RNA expression (P = 0.03), and EGFRvIII-positive CSF-derived EVs had significantly more wtEGFR RNA expression (P = 0.004). EGFRvIII was detected in CSF-derived EVs for 14 of the 23 EGFRvIII tissue-positive GBM patients. Conversely, only one of the 48 EGFRvIII tissue-negative patients had the EGFRvIII mutation detected in their CSF-derived EVs. These results yield a sensitivity of 61% and a specificity of 98% for the utility of CSF-derived EVs to detect an EGFRvIII-positive GBM.
Our results demonstrate CSF-derived EVs contain RNA signatures reflective of the underlying molecular genetic status of GBMs in terms of wtEGFR expression and EGFRvIII status. The high specificity of the CSF-derived EV diagnostic test gives us an accurate determination of positive EGFRvIII tumor status and is essentially a less invasive "liquid biopsy" that might direct mutation-specific therapies for GBMs.
Highlights • Virtual reality (VR) and augmented reality (AR) have great potential in neurosurgery. • Immersive VR has the potential to be used an educational tool. • AR has the added potential of use ...in the live operative field. • Further improvement of VR and AR is crucial to its integration into neurosurgery.
Glioblastoma is a highly aggressive neoplasm and the most common primary malignant brain tumor. Endothelial tissue plays a critical role in glioblastoma growth and progression, facilitating ...angiogenesis, cellular communication, and tumorigenesis. In this review, we present an up-to-date and comprehensive summary of the role of endothelial cells in glioblastomas, along with an overview of recent developments in glioblastoma therapies and tumor endothelial marker identification.
Highlights • Glioblastoma multiforme (GBM) is the most common and deadly primary brain tumor. • CD44 is a transmembrane molecule overexpressed in GBM. • Processes involving CD44 promote GBM invasion, ...proliferation and therapy resistance. • Targeting CD44 is a promising GBM therapy.
Abstract The central nervous system (CNS) historically has been considered an immune-privileged organ, lacking a lymphatic system and shielded from the circulatory system by the blood-brain barrier. ...Microglia are an abundant portion of the CNS cell population, comprising 5% to 20% of the total glial cell population, and are as numerous as neurons. A crucial function of microglia is the ability to generate significant innate and adaptive immune responses. Microglia are involved in first line innate immunity of the CNS. Proper antigen presentation is critical in the generation of specific, durable responses by the adaptive immune system, and requires interaction between the T cell receptor and processed antigen peptide presented on major histocompatibility complex (MHC) molecules by the antigen presenting cells (APC). Microglia also have a large regulatory role in CNS immunity. Histopathologic studies of glioma tissue have consistently shown high levels of infiltrating microglia. Microglia are also localized diffusely throughout the tumor, rather than to the areas of necrosis, and phagocytosis of glioma cells or debris by microglia is not observed. Recent evidence indicates that glioma-infiltrating microglia/macrophages might be promoting tumor growth by facilitating immunosuppression of the tumor microenvironment. When activated, microglia can be potent immune effector cells, able to perform a broad range of functions, and they mediate both innate and adaptive responses during CNS injury and disease while remaining quiescent in the steady state. Their versatility in bridging the gap between the immune-privileged CNS and the peripheral immune system, in addition to their significant numbers in gliomas, makes them an attractive candidate in immunotherapy for gliomas. An enhanced understanding of microglia–glioma interaction may provide better methods to manipulate the glioma microenvironment to allow the generation of a specific and durable anti-glioma immunity. The role of microglia in CNS immunity is reviewed, with a focus on key advances made in glioma immunology.
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