A GPU-accelerated package for simulation of flow in nanoporous source rocks with many-body dissipative particle dynamics

Mesoscopic simulations of hydrocarbon flow in source shales are challenging, in part due to the heterogeneous shale pores with sizes ranging from a few nanometers to a few micrometers. Additionally, the sub-continuum fluid-fluid and fluid-solid interactions in nano- to micro-scale shale pores, which are physically and chemically sophisticated, must be captured. To address those challenges, we present a GPU-accelerated package for simulation of flow in nano- to micro-pore networks with a many-body dissipative particle dynamics (mDPD) mesoscale model. Based on a fully distributed parallel paradigm, the code offloads all intensive workloads on GPUs. Other advancements, such as smart particle packing and no-slip boundary condition in complex pore geometries, are also implemented for the construction and the simulation of the realistic shale pores from 3D nanometer-resolution stack images. Our code is validated for accuracy and compared against the CPU counterpart for speedup. In our benchmark tests, the code delivers nearly perfect strong scaling and weak scaling (with up to 512 million particles) on up to 512 K20X GPUs on Oak Ridge National Laboratory's (ORNL) Titan supercomputer. Moreover, a single-GPU benchmark on ORNL's SummitDev and IBM's AC922 suggests that the host-to-device NVLink can boost performance over PCIe by a remarkable 40\%. Lastly, we demonstrate, through a flow simulation in realistic shale pores, that the CPU counterpart requires 840 Power9 cores to rival the performance delivered by our package with four V100 GPUs on ORNL's Summit architecture. This simulation package enables quick-turnaround and high-throughput mesoscopic numerical simulations for investigating complex flow phenomena in nano- to micro-porous rocks with realistic pore geometries

A Computational Perspective on Network Coding

From the perspectives of graph theory and combinatorics theory we obtain some new upper bounds on the number of encoding nodes, which can characterize the coding complexity of the network coding, both in feasible acyclic and cyclic multicast networks. In contrast to previous work, during our analysis we first investigate the simple multicast network with source rate h=2, and then h≥2. We find that for feasible acyclic multicast networks our upper bound is exactly the lower bound given by M. Langberg et al. in 2006. So the gap between their lower and upper bounds for feasible acyclic multicast networks does not exist. Based on the new upper bound, we improve the computational complexity given by M. Langberg et al. in 2009. Moreover, these results further support the feasibility of signatures for network coding

Prognostic significance of circulating tumor cell measurement in the peripheral blood of patients with nasopharyngeal carcinoma

Objective: Nasopharyngeal Carcinoma (NPC) is lethal cancer. Typically, relapse and metastasis are the outcomes of most patients. Against this backdrop, this study aimed to investigate the correlation between Circulating Tumor Cell (CTC) profiles and clinicopathological features in patients with NPC. Patients and methods: A total of 119 blood samples from 79 patients were collected from patients with NPC during treatment. CanPatrolTM CTC enrichment and RNA In Situ Hybridization (RNA-ISH) were used to characterize CTCs, including epithelial, Mesenchymal (MCTCs), and epithelial/mesenchymal mixed types according to their surface markers. Results: The number of CTCs and MCTCs in the pre-treatment group was significantly higher than that in the post-treatment group (p < 0.05). The total number of CTCs and MCTCs cell numbers was significant correlation with Tumor-Node-Metastasis (TNM) staging (p < 0.05), Progression-Free Survival (PFS), and Overall Survival (OS). The PFS of patients with > 7 CTCs or > 5 MCTCs per 5 mL blood was significantly shorter PFS than those patients with ≤ 7 CTCs or ≤ 5 MCTCs (p < 0.05). Patients treated with targeted therapy combined with chemoradiotherapy had poorer PFS and OS rates than those treated with chemoradiotherapy (p < 0.05). The Kaplan-Meier survival analysis also demonstrated that patients with changes in CTC > 4 were strongly associated with PFS and OS rates (p < 0.05). Conclusion: CTC and MCTC number detection in patients with NPC is a useful biomarker for predicting patient progress. Patients with more than 7 CTCs or 5 MCTCs in 5 mL of blood had shorter PFS and OS rates. CTC and MCTC count changes were also significantly associated with the patient's therapy

Transfusion of Resting Platelets Reduces Brain Hemorrhage After Intracerebral Hemorrhage and tPA-Induced Hemorrhage After Cerebral Ischemia

BackgroundExacerbated blood-brain barrier (BBB) damage is related with tissue plasminogen activator (tPA)-induced brain hemorrhage after stroke. Platelets have long been recognized as the cellular orchestrators of primary haemostasis. Recent studies have demonstrated further that platelets are required for supporting intact mature blood vessels and play a crucial role in maintaining vascular integrity during inflammation. Therefore, we sought to investigate whether platelets could reduce tPA-induced deterioration of cerebrovascular integrity and lead to less hemorrhagic transformation.MethodsMice were subjected to models of collagenase-induced intracerebral hemorrhage (ICH) and transient middle cerebral artery (MCA) occlusion. After 2 h of MCA occlusion, tPA (10 mg/kg) was administered as an intravenous bolus injection of 1 mg/kg followed by a 9 mg/kg infusion for 30 min. Immediately after tPA treatment, mice were transfused with platelets. Hemorrhagic volume, infarct size, neurological deficit, tight junction and basal membrane damages, endothelial cell apoptosis, and extravascular accumulation of circulating dextran and IgG, and Evans blue were quantified at 24 h.ResultsPlatelet transfusion resulted in a significant decrease in hematoma volume after ICH. In mice after ischemia, tPA administration increased brain hemorrhage transformation and this was reversed by resting but not activated platelets. Consistent with this, we observed that tPA-induced brain hemorrhage was dramatically exacerbated in thrombocytopenic mice. Transfusion of resting platelets ameliorated tPA-induced loss of cerebrovascular integrity and reduced extravascular accumulation of circulating serum proteins and Evans blue, associated with improved neurological functions after ischemia. No changes were found for infarct volume. Inhibition of platelet receptor glycoprotein VI (GPVI) blunted the ability of platelets to attenuate tPA-induced BBB disruption and hemorrhage after ischemia.ConclusionOur findings demonstrate the importance of platelets in safeguarding BBB integrity and suggest that transfusion of resting platelets may be useful to improve the safety of tPA thrombolysis in ischemic stroke

Suppression of MAPK11 or HIPK3 reduces mutant Huntingtin levels in Huntington's disease models.

Most neurodegenerative disorders are associated with accumulation of disease-relevant proteins. Among them, Huntington disease (HD) is of particular interest because of its monogenetic nature. HD is mainly caused by cytotoxicity of the defective protein encoded by the mutant Huntingtin gene (HTT). Thus, lowering mutant HTT protein (mHTT) levels would be a promising treatment strategy for HD. Here we report two kinases HIPK3 and MAPK11 as positive modulators of mHTT levels both in cells and in vivo. Both kinases regulate mHTT via their kinase activities, suggesting that inhibiting these kinases may have therapeutic values. Interestingly, their effects on HTT levels are mHTT-dependent, providing a feedback mechanism in which mHTT enhances its own level thus contributing to mHTT accumulation and disease progression. Importantly, knockout of MAPK11 significantly rescues disease-relevant behavioral phenotypes in a knockin HD mouse model. Collectively, our data reveal new therapeutic entry points for HD and target-discovery approaches for similar diseases

Efficient Lossless Compression Based Reversible Data Hiding Using Multilayered n-Bit Localization

We proposed an innovative reversible data hiding technique that is formulated on histogram shifting by using multilayer localized n-bit truncation image (LBPTI), namely, generated form 8-bit plane by means of efficient lossless compression. After selecting the reference point from the block, the neighbor topmost points are used to attain the data embedding without modifying the peak point; in addition, the key information regarding peak point is not mandatory in extraction end to extract the secret information. In order to make the embedded cover-image similar to the histogram of original cover-image, we exploited the localization with efficient lossless compression on lower block level to increase the embedding capacity while controlling extra bit to expand additional embedding capacity on optimum level besides sustaining the quality of cover-image