The technology of large-scale pharmaceutical plasmid purification by cetyltrimethylammonium bromide and Tritonx-114

Many methods for plasmid purification have been developed, and the whole process must be designed to remove the host RNA, protein, genomic DNA and endotoxin. Currently, plasmid is mostly purified by time-consuming chromatographies. As an alternative, a new plasmid purification technology with cetyltrimethylammonium bromide (CTAB) is described. After lysis with alkali, the CTAB was directly titrated into the supernatant for plasmid precipitation, then the coprecipitated pellets were dealt with 3 M KAc and TritonX-114. Quality detection showed that the purified plasmids were free from the contamination of host RNA. In 1 mg purified plasmid, the bacterial genomic DNA, host endotoxin and protein were less than 10 g/ mg, 50 EU/ mg and 10 g/mg, respectively. The ratio of OD260/OD280 was between 1.75 - 1.85, more than 90% of the prepared plasmid presented in the supercoiled form. Further test demonstrated that the pcDNAlacZ purified with CTAB and authoritative endotoxin-free plasmid Kit had the similar transfection efficiency in vivo and in vitro. CTAB can be used for plasmid purification; the main advantages of the DNAs purified with CTAB include the avoidance of animal-derived enzymes, toxic substance like chloroform and phenol. More attractive is that the whole process has the predominance of low cost

Directed Acyclic Graph Continuous Max-Flow Image Segmentation for Unconstrained Label Orderings

Label ordering, the specification of subset–superset relationships for segmentation labels, has been of increasing interest in image segmentation as they allow for complex regions to be represented as a collection of simple parts. Recent advances in continuous max-flow segmentation have widely expanded the possible label orderings from binary background/foreground problems to extendable frameworks in which the label ordering can be specified. This article presents Directed Acyclic Graph Max-Flow image segmentation which is flexible enough to incorporate any label ordering without constraints. This framework uses augmented Lagrangian multipliers and primal–dual optimization to develop a highly parallelized solver implemented using GPGPU. This framework is validated on synthetic, natural, and medical images illustrating its general applicability

A Computationally Efficient Method for Estimating Multi-Model Process Sensitivity Index

Identification of important processes of a hydrologic system is critical for improving process-based hydrologic modeling. To identify important processes while jointly considering parametric and model uncertainty, Dai et al. (2017), https://doi.org/10.1002/2016WR019715, developed a multi-model process sensitivity index. Numerical evaluation of the index using a brute force Monte Carlo (MC) simulation is computationally expensive, because it requires a nested structure of parameter sampling and the number of model simulations is on the order of N-2 (N being the number of parameter samples). To reduce computational cost, we develop a new method (here denoted as quasi-MC for brevity) that uses triple sets of parameter samples (generated using quasi-MC sequence) to remove the nested structure of parameter sampling in a theoretically rigorous way. The quasi-MC method reduces the number of model simulations from the order of N-2 to 2N. The performance of the method is assessed against the brute force MC approach and the recent binning method developed by Dai et al. (2017), https://doi.org/10.1002/2016WR019715, through two synthetic cases of groundwater flow and solute transport modeling. Due to its rigorous theoretical foundation, the quasi-MC method overcomes the limitations imposed by the inherently empirical nature of the binning method. We find that the quasi-MC method outperforms both the brute force MC and the binning method in terms of computational requirements and theoretical aspects, thus strengthening its potential for the assessment of process sensitivity indices subject to various sources of uncertainty

Structural insights into RNA processing by the human RISC-loading complex.

Targeted gene silencing by RNA interference (RNAi) requires loading of a short guide RNA (small interfering RNA (siRNA) or microRNA (miRNA)) onto an Argonaute protein to form the functional center of an RNA-induced silencing complex (RISC). In humans, Argonaute2 (AGO2) assembles with the guide RNA-generating enzyme Dicer and the RNA-binding protein TRBP to form a RISC-loading complex (RLC), which is necessary for efficient transfer of nascent siRNAs and miRNAs from Dicer to AGO2. Here, using single-particle EM analysis, we show that human Dicer has an L-shaped structure. The RLC Dicer's N-terminal DExH/D domain, located in a short 'base branch', interacts with TRBP, whereas its C-terminal catalytic domains in the main body are proximal to AGO2. A model generated by docking the available atomic structures of Dicer and Argonaute homologs into the RLC reconstruction suggests a mechanism for siRNA transfer from Dicer to AGO2

A review of physical supply and EROI of fossil fuels in China

This paper reviews China’s future fossil fuel supply from the perspectives of physical output and net energy output. Comprehensive analyses of physical output of fossil fuels suggest that China’s total oil production will likely reach its peak, at about 230 Mt/year (or 9.6 EJ/year), in 2018; its total gas production will peak at around 350 Bcm/year (or 13.6 EJ/year) in 2040, while coal production will peak at about 4400 Mt/year (or 91.9 EJ/year) around 2020 or so. In terms of the forecast production of these fuels, there are significant differences among current studies. These differences can be mainly explained by different ultimately recoverable resources assumptions, the nature of the models used, and differences in the historical production data. Due to the future constraints on fossil fuels production, a large gap is projected to grow between domestic supply and demand, which will need to be met by increasing imports. Net energy analyses show that both coal and oil and gas production show a steady declining trend of EROI (energy return on investment) due to the depletion of shallow-buried coal resources and conventional oil and gas resources, which is generally consistent with the approaching peaks of physical production of fossil fuels. The peaks of fossil fuels production, coupled with the decline in EROI ratios, are likely to challenge the sustainable development of Chinese society unless new abundant energy resources with high EROI values can be found

Structural modification of TiO2 nanorod films with an influence on the photovoltaic efficiency of a dye-sensitized solar cell (DSSC)

TiO2 nanorod films have been deposited on ITO substrates by dc reactive magnetron sputtering technique. The structures of these nanorod films were modified by the variation of the oxygen pressure during the sputtering process. Although all these TiO2 nanorod films deposited at different oxygen pressures show an anatase structure, the orientation of the nanorod films varies with the oxygen pressure. Only a very weak (101) diffraction peak can be observed for the TiO2 nanorod film prepared at low oxygen pressure. However, as the oxygen pressure is increased, the (220) diffraction peak appears and the intensity of this diffraction peak is increased with the oxygen pressure. The results of the SEM show that these TiO2 nanorods are perpendicular to the ITO substrate. At low oxygen pressure, these sputtered TiO2 nanorods stick together and have a dense structure. As the oxygen pressure is increased, these sputtered TiO2 nanorods get separated gradually and have a porous structure. The optical transmittance of these TiO2 nanorod films has been measured and then fitted by OJL model. The porosities of the TiO2 nanorod films have been calculated. The TiO2 nanorod film prepared at high oxygen pressure shows a high porosity. The dye-sensitized solar cells (DSSCs) have been assembled using these TiO2 nanorod films prepared at different oxygen pressures as photoelectrode. The optimum performance was achieved for the DSSC using the TiO2 nanorod film with the highest (220) diffraction peak and the highest porosity

Spatial and temporal variations of organochlorine pesticides (OCPs) in water and sediments from Honghu Lake, China

Honghu Lake in Jianghan Plain, central China is an important habitat for many migratory birds and an important site for freshwater fishery, and Honghu Lake region is also a main area for rice and cotton production in China. To understand the status and changes of organochlorine pesticide (OCP) contamination, and to assess the OCPs' risks for the ecosystem in Honghu Lake, thirty surface water samples, fifteen surface sediments, and a sediment core were collected in January and July, 2005. OCPs, such as DDTs, HCHs and chlordanes, were determined by GC-ECD in all samples. Concentrations of OCPs in surface water collected during the wet season (July 2005) were relatively higher than those collected during the dry season (January 2005), indicating that the increasing land runoff during the summer might bring the chemical residues from soils to Honghu Lake. The relatively low alpha-HCH/gamma-HCH ratio and the relatively high o,p'-DDT/p,p'-DDT ratio indicated the application of lindane on regional agricultural lands in late spring and summer (April-August), which increased the increasing contribution of dicofol to DDT in Honghu Lake, respectively. The levels of Sigma HCHs and Sigma DDTs in the surface sediments were relatively lower than those from the Yangtze River Delta, but comparable to those from other lakes and rivers in China. The composition of HCHs and DDTs in the surface sediments showed that there was fresh input of lindane (gamma-HCH), and DDT residues in Honghu Lake were aged and probably mainly originated from weathered agricultural soils of surrounding Jianghan Plain. Wash out of HCHs and DDTs from soil was the possible process which caused the increasing concentrations of these chemicals in recent years. (C) 2013 Elsevier B.V. All rights reserved.Honghu Lake in Jianghan Plain, central China is an important habitat for many migratory birds and an important site for freshwater fishery, and Honghu Lake region is also a main area for rice and cotton production in China. To understand the status and changes of organochlorine pesticide (OCP) contamination, and to assess the OCPs' risks for the ecosystem in Honghu Lake, thirty surface water samples, fifteen surface sediments, and a sediment core were collected in January and July, 2005. OCPs, such as DDTs, HCHs and chlordanes, were determined by GC-ECD in all samples. Concentrations of OCPs in surface water collected during the wet season (July 2005) were relatively higher than those collected during the dry season (January 2005), indicating that the increasing land runoff during the summer might bring the chemical residues from soils to Honghu Lake. The relatively low alpha-HCH/gamma-HCH ratio and the relatively high o,p'-DDT/p,p'-DDT ratio indicated the application of lindane on regional agricultural lands in late spring and summer (April-August), which increased the increasing contribution of dicofol to DDT in Honghu Lake, respectively. The levels of Sigma HCHs and Sigma DDTs in the surface sediments were relatively lower than those from the Yangtze River Delta, but comparable to those from other lakes and rivers in China. The composition of HCHs and DDTs in the surface sediments showed that there was fresh input of lindane (gamma-HCH), and DDT residues in Honghu Lake were aged and probably mainly originated from weathered agricultural soils of surrounding Jianghan Plain. Wash out of HCHs and DDTs from soil was the possible process which caused the increasing concentrations of these chemicals in recent years. (C) 2013 Elsevier B.V. All rights reserved

Deep learning enables spatial mapping of the mosaic microenvironment of myeloma bone marrow trephine biopsies

Bone marrow trephine biopsy is crucial for the diagnosis of multiple myeloma. However, the complexity of bone marrow cellular, morphological, and spatial architecture preserved in trephine samples hinders comprehensive evaluation. To dissect the diverse cellular communities and mosaic tissue habitats, we developed a superpixel-inspired deep learning method (MoSaicNet) that adapts to complex tissue architectures and a cell imbalance aware deep learning pipeline (AwareNet) to enable accurate detection and classification of rare cell types in multiplex immunohistochemistry images. MoSaicNet and AwareNet achieved an area under the curve of >0.98 for tissue and cellular classification on separate test datasets. Application of MoSaicNet and AwareNet enabled investigation of bone heterogeneity and thickness as well as spatial histology analysis of bone marrow trephine samples from monoclonal gammopathies of undetermined significance (MGUS) and from paired newly diagnosed and post-treatment multiple myeloma. The most significant difference between MGUS and newly diagnosed multiple myeloma (NDMM) samples was not related to cell density but to spatial heterogeneity, with reduced spatial proximity of BLIMP1+ tumor cells to CD8+ cells in MGUS compared with NDMM samples. Following treatment of multiple myeloma patients, there was a reduction in the density of BLIMP1+ tumor cells, effector CD8+ T cells, and T regulatory cells, indicative of an altered immune microenvironment. Finally, bone heterogeneity decreased following treatment of MM patients. In summary, deep-learning based spatial mapping of bone marrow trephine biopsies can provide insights into the cellular topography of the myeloma marrow microenvironment and complement aspirate-based techniques

Thunderclap headache triggered by micturition: responsive to nimodipine

Primary thunderclap headache (TCH) is a rare condition, of which the onset can be triggered by coughing, exercise, and sexual activity. Micturition is a recognized trigger of secondary TCH with pheochromocytoma in bladder, but not of primary TCH. We describe a patient with an apparent primary TCH, which repeatedly occurred immediately after micturition until she achieved a therapeutic dosage of nimodipine