Subspace projection approaches to classification and visualization of neural network-level encoding patterns

Recent advances in large-scale ensemble recordings allow monitoring of activity patterns of several hundreds of neurons in freely behaving animals. The emergence of such high-dimensional datasets poses challenges for the identification and analysis of dynamical network patterns. While several types of multivariate statistical methods have been used for integrating responses from multiple neurons, their effectiveness in pattern classification and predictive power has not been compared in a direct and systematic manner. Here we systematically employed a series of projection methods, such as Multiple Discriminant Analysis (MDA), Principal Components Analysis (PCA) and Artificial Neural Networks (ANN), and compared them with non-projection multivariate statistical methods such as Multivariate Gaussian Distributions (MGD). Our analyses of hippocampal data recorded during episodic memory events and cortical data simulated during face perception or arm movements illustrate how low-dimensional encoding subspaces can reveal the existence of network-level ensemble representations. We show how the use of regularization methods can prevent these statistical methods from over-fitting of training data sets when the trial numbers are much smaller than the number of recorded units. Moreover, we investigated the extent to which the computations implemented by the projection methods reflect the underlying hierarchical properties of the neural populations. Based on their ability to extract the essential features for pattern classification, we conclude that the typical performance ranking of these methods on under-sampled neural data of large dimension is MDA>PCA>ANN>MGD.     

Multimetal resistance and tolerance in microbial biofilms

Geochemical cycling and industrial pollution have made toxic metal ions a pervasive environmental pressure throughout the world. Biofilm formation is a strategy that microorganisms might use to survive a toxic flux in these inorganic compounds. Evidence in the literature suggests that biofilm populations are protected from toxic metals by the combined action of chemical, physical and physiological phenomena that are, in some instances, linked to phenotypic variation among the constituent biofilm cells. Here, we propose a multifactorial model by which biofilm populations can withstand metal toxicity by a process of cellular diversification.     

Quantification of urinary zwitterionic organic acids using weak-anion exchange chromatography with tandem MS detection

A rapid and accurate quantitative method was developed and validated for the analysis of four urinary organic acids with nitrogen containing functional groups, formiminoglutamic acid (FIGLU), pyroglutamic acid (PYRGLU), 5-hydroxyindoleacetic acid (5-HIAA), and 2-methylhippuric acid (2-METHIP) by liquid chromatography tandem mass spectrometry (LC/MS/MS). The chromatography was developed using a weak anion-exchange amino column that provided mixed-mode retention of the analytes. The elution gradient relied on changes in mobile phase pH over a concave gradient, without the use of counter-ions or concentrated salt buffers. A simple sample preparation was used, only requiring the dilution of urine prior to instrumental analysis. The method was validated based on linearity (r2>or=0.995), accuracy (85-115%), precision (C.V.<12%), sample preparation stability (相似文献   

Analysis of NVMe over fabrics with SCinet DTN-as-a-Service

Supporting transfers of science big data over Wide Area Networks (WANs) with Data Transfer Nodes (DTNs) requires optimizing multiple parameters within the underlying infrastructure. New solutions for such data movement require new paradigms and technologies, such as NVMe over Fabrics, which provides high-performance data movement with direct remote NVMe device access over traditional fabrics. However, recent NVMe over Fabrics studies have been limited to local storage fabrics. To support increasing demands for the large volume of science data movement during Supercomputing (SC) conferences, we proposed a SCinet DTN-as-a-Service framework orchestrating the desired optimization to meet users, applications, and providers’ requirements. Furthermore, we extend the SCinet DTN-as-a-Service framework to incorporate new techniques, solve optimization issues in data-intensive science and evaluate NVMe over Fabrics with multiple WAN testbeds to examine its performance and discover new opportunities for optimization.

     

Natural killer cells kill extracellular Pseudomonas aeruginosa using contact-dependent release of granzymes B and H

Pseudomonas aeruginosa is an opportunistic pathogen that often infects individuals with the genetic disease cystic fibrosis, and contributes to airway blockage and loss of lung function. Natural killer (NK) cells are cytotoxic, granular lymphocytes that are part of the innate immune system. NK cell secretory granules contain the cytolytic proteins granulysin, perforin and granzymes. In addition to their cytotoxic effects on cancer and virally infected cells, NK cells have been shown to play a role in an innate defense against microbes, including bacteria. However, it is not known if NK cells kill extracellular P. aeruginosa or how bacterial killing might occur at the molecular level. Here we show that NK cells directly kill extracellular P. aeruginosa using NK effector molecules. Live cell imaging of a co-culture of YT cells, a human NK cell line, and GFP-expressing P. aeruginosa in the presence of the viability dye propidium iodide demonstrated that YT cell killing of P. aeruginosa is contact-dependent. CRISPR knockout of granulysin or perforin in YT cells had no significant effect on YT cell killing of P. aeruginosa. Pre-treatment of YT and NK cells with the serine protease inhibitor 3,4-dichloroisocoumarin (DCI) to inhibit all granzymes, resulted in an inhibition of killing. Although singular CRISPR knockout of granzyme B or H had no effect, knockout of both in YT cells completely abrogated killing of P. aeruginosa in comparison to wild type YT cell controls. Nitrocefin assays suggest that the bacterial membrane is damaged. Inhibition of killing by antioxidants suggest that ROS are required for the bactericidal mode-of-action. Taken together, these results identify that NK cells kill P. aeruginosa through a membrane damaging, contact-dependent process that requires granzyme induced ROS production, and moreover, that granzyme B and H are redundant in this killing process.     

Neurovascular congruence results from a shared patterning mechanism that utilizes Semaphorin3A and Neuropilin-1

Peripheral nerves and blood vessels have similar patterns in quail forelimb development. Usually, nerves extend adjacent to existing blood vessels, but in a few cases, vessels follow nerves. Nerves have been proposed to follow vascular smooth muscle, endothelium, or their basal laminae. Focusing on the major axial blood vessels and nerves, we found that when nerves grow into forelimbs at E3.5-E5, vascular smooth muscle was not detectable by smooth muscle actin immunoreactivity. Additionally, transmission electron microscopy at E5.5 confirmed that early blood vessels lacked smooth muscle and showed that the endothelial cell layer lacks a basal lamina, and we did not observe physical contact between peripheral nerves and these endothelial cells. To test more generally whether lack of nerves affected blood vessel patterns, forelimb-level neural tube ablations were performed at E2 to produce aneural limbs; these had completely normal vascular patterns up to at least E10. To test more generally whether vascular perturbation affected nerve patterns, VEGF(165), VEGF(121), Ang-1, and soluble Flt-1/Fc proteins singly and in combination were focally introduced via beads implanted into E4.5 forelimbs. These produced significant alterations to the vascular patterns, which included the formation of neo-vessels and the creation of ectopic avascular spaces at E6, but in both under- and overvascularized forelimbs, the peripheral nerve pattern was normal. The spatial distribution of semaphorin3A protein immunoreactivity was consistent with a negative regulation of neural and/or vascular patterning. Semaphorin3A bead implantations into E4.5 forelimbs caused failure of nerves and blood vessels to form and to deviate away from the bead. Conversely, semaphorin3A antibody bead implantation was associated with a local increase in capillary formation. Furthermore, neural tube electroporation at E2 with a construct for the soluble form of neuropilin-1 caused vascular malformations and hemorrhage as well as altered nerve trajectories and peripheral nerve defasciculation at E5-E6. These results suggest that neurovascular congruency does not arise from interdependence between peripheral nerves and blood vessels, but supports the hypothesis that it arises by a shared patterning mechanism that utilizes semaphorin3A.     

Phosphorylation-regulated cleavage of the tumor suppressor PTEN by caspase-3: implications for the control of protein stability and PTEN-protein interactions

PTEN phosphatase is one of the most commonly targeted tumor suppressors in human cancers and a key regulator of cell growth and apoptosis. We have found that PTEN is cleaved by caspase-3 at several target sites, located in unstructured regions within the C terminus of the molecule. Cleavage of PTEN was increased upon TNFalpha-cell treatment and was negatively regulated by phosphorylation of the C-terminal tail of PTEN by the protein kinase CK2. The proteolytic PTEN fragments displayed reduced protein stability, and their capability to interact with the PTEN interacting scaffolding protein S-SCAM/MAGI-2 was lost. Interestingly, S-SCAM/MAGI-2 was also cleaved by caspase-3. Our findings suggest the existence of a regulatory mechanism of protein stability and PTEN-protein interactions during apoptosis, executed by caspase-3 in a PTEN phosphorylation-regulated manner.     

Specific interaction of protein tyrosine phosphatase-MEG2 with phosphatidylserine

Protein tyrosine phosphatase (PTP)-MEG2 is an intracellular tyrosine phosphatase that contains a Sec14 homology domain. We have purified the full-length and truncated forms of the enzyme from recombinant adenovirus-infected human 293 cells. By using lipid-membrane overlay and liposome binding assays, we demonstrated that PTP-MEG2 specifically binds phosphatidylserine among over 20 lipid compounds tested. The binding is mediated by its N-terminal Sec14 domain. In intact cells, the Sec14 domain is responsible for localization of PTP-MEG2 to the perinuclear region, and uploading of PS into the cell membrane causes translocation of PTP-MEG2 to the plasma membrane. Phosphatidylserine is a relatively abundant cell membrane phospholipid non-symmetrically distributed in the outer layer and inner layer of cell membranes. It has recently been defined as an important ligand for clearance of apoptotic cells. By specifically binding phosphatidylserine, PTP-MEG2 may play an important role in regulating signaling processes associated with phagocytosis of apoptotic cells.