Interferometric detection and enumeration of viral particles using Si-based microfluidics

Single-particle interferometric reflectance imaging sensor enables optical visualization and characterization of individual nanoparticles without any labels. Using this technique, we have shown end-point and real-time detection of viral particles using laminate-based active and passive cartridge configurations. Here, we present a new concept for low-cost microfluidic integration of the sensor chips into compact cartridges through utilization of readily available silicon fabrication technologies. This new cartridge configuration will allow simultaneous detection of individual virus binding events on a 9-spot microarray, and provide the needed simplicity and robustness for routine real-time operation for discrete detection of viral particles in a multiplex format.This work was supported in part by a research contract with the ASELSAN Research Center, Ankara, Turkey, and in part by the European Union's Horizon 2020 FET Open program under Grant 766466-INDEX. (ASELSAN Research Center, Ankara, Turkey; 766466-INDEX - European Union's Horizon 2020 FET Open program)First author draf

JDFTx: software for joint density-functional theory

Density-functional theory (DFT) has revolutionized computational prediction of atomic-scale properties from first principles in physics, chemistry and materials science. Continuing development of new methods is necessary for accurate predictions of new classes of materials and properties, and for connecting to nano- and mesoscale properties using coarse-grained theories. JDFTx is a fully-featured open-source electronic DFT software designed specifically to facilitate rapid development of new theories, models and algorithms. Using an algebraic formulation as an abstraction layer, compact C++11 code automatically performs well on diverse hardware including GPUs. This code hosts the development of joint density-functional theory (JDFT) that combines electronic DFT with classical DFT and continuum models of liquids for first-principles calculations of solvated and electrochemical systems. In addition, the modular nature of the code makes it easy to extend and interface with, facilitating the development of multi-scale toolkits that connect to ab initio calculations, e.g. photo-excited carrier dynamics combining electron and phonon calculations with electromagnetic simulations.Comment: 9 pages, 3 figures, 2 code listing

Numerical Model for the Determination of Erythrocyte Mechanical Properties and Wall Shear Stress in vivo From Intravital Microscopy.

The mechanical properties and deformability of Red Blood Cells (RBCs) are important determinants of blood rheology and microvascular hemodynamics. The objective of this study is to quantify the mechanical properties and wall shear stress experienced by the RBC membrane during capillary plug flow in vivo utilizing high speed video recording from intravital microscopy, biomechanical modeling, and computational methods. Capillaries were imaged in the rat cremaster muscle pre- and post-RBC transfusion of stored RBCs for 2-weeks. RBC membrane contours were extracted utilizing image processing and parametrized. RBC parameterizations were used to determine updated deformation gradient and Lagrangian Green strain tensors for each point along the parametrization and for each frame during plug flow. The updated Lagrangian Green strain and Displacement Gradient tensors were numerically fit to the Navier-Lame equations along the parameterized boundary to determined Lame's constants. Mechanical properties and wall shear stress were determined before and transfusion, were grouped in three populations of erythrocytes: native cells (NC) or circulating cells before transfusion, and two distinct population of cells after transfusion with stored cells (SC1 and SC2). The distinction, between the heterogeneous populations of cells present after the transfusion, SC1 and SC2, was obtained through principle component analysis (PCA) of the mechanical properties along the membrane. Cells with the first two principle components within 3 standard deviations of the mean, were labeled as SC1, and those with the first two principle components greater than 3 standard deviations from the mean were labeled as SC2. The calculated shear modulus average was 1.1±0.2, 0.90±0.15, and 12 ± 8 MPa for NC, SC1, and SC2, respectively. The calculated young's modulus average was 3.3±0.6, 2.6±0.4, and 32±20 MPa for NC, SC1, and SC2, respectively. o our knowledge, the methods presented here are the first estimation of the erythrocyte mechanical properties and shear stress in vivo during capillary plug flow. In summary, the methods introduced in this study may provide a new avenue of investigation of erythrocyte mechanics in the context of hematologic conditions that adversely affect erythrocyte mechanical properties

Highly sensitive and label-free digital detection of whole cell E. coli with interferometric reflectance imaging

Bacterial infectious diseases are a major threat to human health. Timely and sensitive pathogenic bacteria detection is crucial in identifying the bacterial contaminations and preventing the spread of infectious diseases. Due to limitations of conventional bacteria detection techniques there have been concerted research efforts towards development of new biosensors. Biosensors offering label free, whole bacteria detection are highly desirable over those relying on label based or pathogenic molecular components detection. The major advantage is eliminating the additional time and cost required for labeling or extracting the desired bacterial components. Here, we demonstrate rapid, sensitive and label free E. coli detection utilizing interferometric reflectance imaging enhancement allowing for visualizing individual pathogens captured on the surface. Enabled by our ability to count individual bacteria on a large sensor surface, we demonstrate a limit of detection of 2.2 CFU/ml from a buffer solution with no sample preparation. To the best of our knowledge, this high level of sensitivity for whole E. coli detection is unprecedented in label free biosensing. The specificity of our biosensor is validated by comparing the response to target bacteria E. coli and non target bacteria S. aureus, K. pneumonia and P. aeruginosa. The biosensor performance in tap water also proves that its detection capability is unaffected by the sample complexity. Furthermore, our sensor platform provides high optical magnification imaging and thus validation of recorded detection events as the target bacteria based on morphological characterization. Therefore, our sensitive and label free detection method offers new perspectives for direct bacterial detection in real matrices and clinical samples.First author draf

A CONDUCTING COMPOSITE OF POLYPYRROLE .1. SYNTHESIS AND CHARACTERIZATION

A conducting composite of polypyrrole was prepared via electrochemical methods. A polyamide was used as the insulating matrix polymer. The characterization of the composite was done by FT-IR, SEM, TGA, DSC and pyrolysis studies. Conductivity and solubility studies together with spectroscopic methods reveal that H bonding exists between the two polymers and a possible grafting to a certain extent

Almost-zero logic implementation of Troika hash function on reconfigurable devices

Blockchain technology has gained immense popularity in the recent years due to its decentralized computing architecture. While it originally emerged as a technology for (crypto)currencies, it has since found many different application areas including (but not limited to) payments, money transfers, smart contracts, supply-chain management, networking, IoT, etc. Initially, it was only Bitcoin, the de facto standard for cryptocurrencies, but then it was followed by several (in fact hundreds of) others. Each new cryptocurrency had or claimed to have certain advantages over Bitcoin, such as transaction speed and cost. However, they all relied on the original idea of distributed ledger where each block has maintained a complete history of each transaction in the network. Blockchain technology has more recently been challenged by two new technologies called Tangle and Hashgraph, which are “directed acyclic graphs”, i.e. in layman's terms blockchains without blocks and chains. IOTA network is the original Tangle technology, which relies on ternary arithmetic architecture and uses ternary hash function “Troika”. It works on GF(3) and its design follows the sponge construction. Two of the main claims of IOTA are scalability and micro-transitions, both of which are likely to utilize compact hardware platforms in practical implementations. In this paper, an almost-zero logic compact and yet adequately fast hardware architectures of Troika hash function targeting reconfigurable devices are presented. The proposed architectures mainly depend on the utilization of BRAMs on FPGAs. Three different RAM-based hardware implementations have been realized on Xilinx Artix-7xc7a12tcpg238-3 device; all using only a single BRAM tile with minimal number of LUTs and FFs. The proposed architectures can easily be implemented on different reconfigurable devices with similar efficiency. To the best of our knowledge, this is the first reported hardware implementation of Troika hash function on reconfigurable devices which is also compact and fast

Identification of tissue-specific microRNAs from mouse

MicroRNAs (miRNAs) are a new class of noncoding RNAs, which are encoded as short inverted repeats in the genomes of invertebrates and vertebrates [1, 2]. It is believed that miRNAs are modulators of target mRNA translation and stability, although most target mRNAs remain to be identified. Here we describe the identification of 34 novel miRNAs by tissue- specific cloning of approximately 21-nucleotide RNAs from mouse. Almost all identified miRNAs are conserved in the human genome and are also frequently found in nonmammalian vertebrate genomes, such as pufferfish. In heart, liver, or brain, it is found that a single, tissue-specifically expressed miRNA dominates the population of expressed miRNAs and suggests a role for these miRNAs in tissue specification or cell lineage decisions. Finally, a miRNA was identified that appears to be the fruitfly and mammalian ortholog of C. elegans lin-4 stRNA

A sustainable method of effluent disposal: case study of Antalya sea outfall, Turkey

Antalya city, located along the Turkish Mediterranean coast, lacked a proper sanitation system till 1996. An integrated water & wastewater project has been implemented to protect groundwater resources used for drinking and seawater quality. The project involved collection, treatment and final disposal of effluents by a deep sea outfall system. A current research project has been realized to evaluate performance of Antalya Sea Outfall. Seasonal in-situ measurements and bacteriological monitoring studies have been realized. The discharged wastewater plume is observed to be submerged in summer and to reach sea surface in winter condition. The results of the monitoring program exhibit considerable spatial and temporal variations. The resultant total and fecal coliform numbers comply well with the Turkish Standards for the use of coastal and sea water for recreation