High-Performance Multi-Mode Ptychography Reconstruction on Distributed GPUs

Ptychography is an emerging imaging technique that is able to provide wavelength-limited spatial resolution from specimen with extended lateral dimensions. As a scanning microscopy method, a typical two-dimensional image requires a number of data frames. As a diffraction-based imaging technique, the real-space image has to be recovered through iterative reconstruction algorithms. Due to these two inherent aspects, a ptychographic reconstruction is generally a computation-intensive and time-consuming process, which limits the throughput of this method. We report an accelerated version of the multi-mode difference map algorithm for ptychography reconstruction using multiple distributed GPUs. This approach leverages available scientific computing packages in Python, including mpi4py and PyCUDA, with the core computation functions implemented in CUDA C. We find that interestingly even with MPI collective communications, the weak scaling in the number of GPU nodes can still remain nearly constant. Most importantly, for realistic diffraction measurements, we observe a speedup ranging from a factor of $10$ to $10^3$ depending on the data size, which reduces the reconstruction time remarkably from hours to typically about 1 minute and is thus critical for real-time data processing and visualization.Comment: work presented in NYSDS 201

CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse

Diversified histone modifications (HMs) are essential epigenetic features. They play important roles in fundamental biological processes including transcription, DNA repair and DNA replication. Chromatin regulators (CRs), which are indispensable in epigenetics, can mediate HMs to adjust chromatin structures and functions. With the development of ChIP-Seq technology, there is an opportunity to study CR and HM profiles at the whole-genome scale. However, no specific resource for the integration of CR ChIP-Seq data or CR-HM ChIP-Seq linkage pairs is currently available. Therefore, we constructed the CR Cistrome database, available online at http://compbio.tongji.edu.cn/cr and http://cistrome.org/cr/, to further elucidate CR functions and CR-HM linkages. Within this database, we collected all publicly available ChIP-Seq data on CRs in human and mouse and categorized the data into four cohorts: the reader, writer, eraser and remodeler cohorts, together with curated introductions and ChIP-Seq data analysis results. For the HM readers, writers and erasers, we provided further ChIP-Seq analysis data for the targeted HMs and schematized the relationships between them. We believe CR Cistrome is a valuable resource for the epigenetics community

Complete Strain Mapping of Nanosheets of Tantalum Disulfide

Quasi-two-dimensional (quasi-2D) materials hold promise for future electronics because of their unique band structures that result in electronic and mechanical properties sensitive to crystal strains in all three dimensions. Quantifying crystal strain is a prerequisite to correlating it with the performance of the device, and calls for high resolution but spatially resolved rapid characterization methods. Here we show that using fly-scan nano X-ray diffraction we can accomplish a tensile strain sensitivity below 0.001% with a spatial resolution of better than 80 nm over a spatial extent of 100 $\mu$m on quasi 2D flakes of 1T-TaS2. Coherent diffraction patterns were collected from a $\sim$ 100 nm thick sheet of 1T-TaS2 by scanning 12keV focused X-ray beam across and rotating the sample. We demonstrate that the strain distribution around micron and sub-micron sized 'bubbles' that are present in the sample may be reconstructed from these images. The experiments use state of the art synchrotron instrumentation, and will allow rapid and non-intrusive strain mapping of thin film samples and electronic devices based on quasi 2D materials

Self-absorption correction on 2D X-ray fluorescence maps

Abstract X-ray fluorescence mapping (XRF) is a highly efficient and non-invasive technique for quantifying material composition with micro and nanoscale spatial resolutions. Quantitative XRF analysis, however, confronts challenges from the long-lasting problem called self-absorption. Moreover, correcting two-dimensional XRF mapping datasets is particularly difficult because it is an ill-posed inverse problem. Here we report a semi-empirical method that can effectively correct 2D XRF mapping data. The correction error is generally less than 10% from a comprehensive evaluation of the accuracy in various configurations. The proposed method was applied to quantify the composition distribution around the grain boundaries in an electrochemically corroded stainless steel sample. Highly localized Cr enrichment was found around the crack sites, which was invisible before the absorption correction

A positive-feedback loop between HBx and ALKBH5 promotes hepatocellular carcinogenesis

Abstract Background Hepatitis B Virus (HBV) contributes to liver carcinogenesis via various epigenetic mechanisms. The newly defined epigenetics, epitranscriptomics regulation, has been reported to involve in multiple cancers including Hepatocellular Carcinoma (HCC). Our previous study found that HBx, HBV encodes X protein, mediated H3K4me3 modification in WDR5-dependent manner to involve in HBV infection and contribute to oncogene expression. AlkB Homolog 5 (ALKBH5), one of epitranscriptomics enzymes, has been identified to be associated with various cancers. However, whether and how ALKBH5 is dysregulated in HBV-related HCC remains unclear yet. This study aims to investigate ALKBH5 function, clinical significance and mechanism in HBV related HCC (HBV-HCC) patients derived from Chinese people. Methods The expression pattern of ALKBH5 was evaluated by RT-qPCR, Western blot, data mining and immunohistochemistry in total of 373 HBV-HCC tissues and four HCC cell lines. Cell Counting Kit 8 (CCK8) assay, Transwell and nude mouse model were performed to assess ALKBH5 function by both small interference RNAs and lentiviral particles. The regulation mechanism of ALKBH5 was determined in HBx and WDR5 knockdown cells by CHIP-qPCR. The role of ALKBH5 in HBx mRNA N6-methyladenosine (m6A) modification was further evaluated by MeRIP-qPCR and Actinomycin D inhibitor experiment in HBV-driven cells and HBx overexpression cells. Result ALKBH5 increased in tumor tissues and predicts a poor prognosis of HBV-HCC. Mechanically, the highly expressed ALKBH5 is induced by HBx-mediated H3K4me3 modification of ALKBH5 gene promoter in a WDR5-dependent manner after HBV infection. The increased ALKBH5 protein catalyzes the m6A demethylation of HBx mRNA, thus stabilizing and favoring a higher HBx expression level. Furthermore, there are positive correlations between HBx and ALKBH5 in HBV-HCC tissues, and depletion of ALKBH5 significantly inhibits HBV-driven tumor cells’ growth and migration in vitro and in vivo. Conclusions HBx-ALKBH5 may form a positive-feedback loop to involve in the HBV-induced liver carcinogenesis, and targeting the loop at ALKBH5 may provide a potential way for HBV-HCC treatment

Protective Effects of Ischemic Preconditioning Protocols on Ischemia-Reperfusion Injury in Rat Liver

Background: Hepatic ischemia reperfusion injury often leads to increased complications and mortality after surgery. Although ischemic preconditioning is used as a convenient and effective method to protect the liver from warm ischemia reperfusion injury, the optimal protocol is currently unclear. Therefore, in this study, we sought to identify ideal conditions and methods for ischemic preconditioning. Materials and methods: We compared several preconditioning protocols of the ischemia/reperfusion (I/R) cycle in 30 male Sprague-Dawley rats (5 groups, n = 6), including relevant sham and I/R injury (no preconditioning) controls. Experimental group conditions included: (1) ischemia for 5 min/reperfusion for 10 min (ischemic preconditioning 1, IPC-1); (2) ischemia for 5 min/reperfusion for 5 min, repeated three times (IPC-2); and (3) ischemia for 10 min/reperfusion for 10 min (IPC-3). Readouts included transaminase activity levels measured from collected sera, and histopathological changes, liver cell apoptosis, superoxide dismutase (SOD) activity, glutathione (GSH) levels, and malondialdehyde (MDA) levels measured from collected liver tissue segments subjected to warm ischemia (that is from the 70% of the liver mass that had been deprived from blood flow during the ischemia phase). Results: Compared to the I/R control group, the IPC-1, IPC-2, and IPC-3 groups all showed significant decreases in liver transaminase activity levels, alleviation of pathological injury-associated changes, and a decrease in liver cell apoptosis. Moreover, SOD activity and GSH content were increased while MDA content was decreased in the three experimental groups. Compared to the IPC-1 and IPC-3 groups, the changes in the IPC-2 group were the most significant (P < 0.05). Conclusions: Ischemic preconditioning can reduce hepatic warm ischemia reperfusion injury in rats. The IPC-2 protocol, involving ischemia for 5 min and reperfusion for 5 min, repeated three times, provided the optimal protection against hepatic ischemia reperfusion injury among the protocols studied

RBBP7, regulated by SP1, enhances the Warburg effect to facilitate the proliferation of hepatocellular carcinoma cells via PI3K/AKT signaling

Abstract Background Hepatocellular carcinoma (HCC) is characterized by aggressive progression and elevated mortality rates. This study aimed to investigate the regulatory effects of RBBP7 on HCC pathogenesis and the underlying mechanisms. Methods The expression and clinical feature of RBBP7 were evaluated using bioinformatics analysis and the assessment of clinical HCC samples. CCK8 and colony formation were employed to estimate cell proliferation function of RBBP7. Aerobic glycolysis levels of RBBP7 were evaluated by measuring ATP levels, lactic acid production, glucose uptake capacity, and the expression of relevant enzymes (PFKM, PKM2, and LDHA). The phosphorylation levels in PI3K/AKT signaling were measured by western blotting. The regulatory effect of transcription factors of specificity protein 1 (SP1) on RBBP7 mRNA expression was confirmed in dual-luciferase reporter assays and chromatin immunoprecipitation experiments. The proliferation- and glycolysis-associated proteins were assessed using immunofluorescence staining in vivo. Results We found that RBBP7 is expressed at high levels in HCC and predicts poor survival. Functional assays showed that RBBP7 promoted HCC proliferation and glycolysis. Mechanistically, it was demonstrated that RBBP7 activates the PI3K/AKT pathway, a crucial pathway in glycolysis, contributing to the progression of HCC. The outcomes of the dual-luciferase assay further confirmed that SP1 is capable of activating the promoter of RBBP7. Conclusions RBBP7, which is up-regulated by SP1, promotes HCC cell proliferation and glycolysis through the PI3K/AKT pathway. The findings of this study suggest that RBBP7 is a potential biomarker for HCC

Electrocatalytic mechanism of titanium-based anodes and research progress of chemical saline wastewater treatment: A short review

Electrocatalytic treatment of chemical saline wastewater showed great technical advantages due to its characteristics of simple operation, high catalytic efficiency and little secondary pollution. The review takes the classification and composition of titanium-based anodes as the starting point. Typical studies of wastewater treatment by electrocatalytic technology based on free radicals and non-free radicals were also discussed. Combined with the previous researches about electrocatalytic mechanisms in recent years, the mechanisms of titanium-based anodes were analyzed in terms of ·OH, active chlorine and others. The studies on titanium-based anodes in chemical wastewater containing different salt concentrations, such as dye wastewater, coal chemical wastewater, landfill leachate wastewater, fertilizer and pesticide production wastewater, etc., were thoroughly examined. According to the amount of electricity required for the removal of organic matter per unit, the energy consumption of titanium-based anodes for wastewater treatment by electrochemistry was described. The review would provide theoretical basis and technical support for electrocatalytic treatment of chemical saline wastewater