The distributed particle detectors and data acquisition modules for Extensive Air Shower measurements at "HT-KZ" experiment

"HorizonT-Kazakhstan" (HT-KZ) is an extensive air shower new detector system of a new type to be constructed at Nazarbayev University (NU), Astana, KZ. It is based on the idea of a previous generation detector that is located at Tyan-Shan high-altitude Science Station of the Physical Institute of Russian science academy at approximately 3340 meters above the sea level. It will consist of 8 independent modules distributed on the roofs of NU with 1-2ns time resolution. The purpose is to register Extensive Air Showers (EAS) coming from a wide range of zenith angles. The measurements of the time characteristics of the EAS are to be taken simultaneously at up to eight registration points separated by the distance up to one kilometer. HT-KZ development is very important step in the EAS research area, especially, in the presence of the last connected discoveries, such as multi-modal events This article presents the current system development state, the R&D work of the system modules using the independent particle detection modules. The distributed DAQ system and event synchronization system progress will be discussed as wel

The pumping lid: investigating multi-material 3D printing for equipment-free, programmable generation of positive and negative pressures for microfluidic applications

Equipment-free pumping is a challenging problem and an active area of research in microfluidics, with applications for both laboratory and limited-resource settings. This paper describes the pumping lid method, a strategy to achieve equipment-free pumping by controlled generation of pressure. Pressure was generated using portable, lightweight, and disposable parts that can be integrated with existing microfluidic devices to simplify workflow and eliminate the need for pumping equipment. The development of this method was enabled by multi-material 3D printing, which allows fast prototyping, including composite parts that combine materials with different mechanical properties (e.g. both rigid and elastic materials in the same part). The first type of pumping lid we describe was used to produce predictable positive or negative pressures via controlled compression or expansion of gases. A model was developed to describe the pressures and flow rates generated with this approach and it was validated experimentally. Pressures were pre-programmed by the geometry of the parts and could be tuned further even while the experiment was in progress. Using multiple lids or a composite lid with different inlets enabled several solutions to be pumped independently in a single device. The second type of pumping lid, which relied on vapor–liquid equilibrium to generate pressure, was designed, modeled, and experimentally characterized. The pumping lid method was validated by controlling flow in different types of microfluidic applications, including the production of droplets, control of laminar flow profiles, and loading of SlipChip devices. We believe that applying the pumping lid methodology to existing microfluidic devices will enhance their use as portable diagnostic tools in limited resource settings as well as accelerate adoption of microfluidics in laboratories

Reading Out Single-Molecule Digital RNA and DNA Isothermal Amplification in Nanoliter Volumes with Unmodified Camera Phones

Digital single-molecule technologies are expanding diagnostic capabilities, enabling the ultrasensitive quantification of targets, such as viral load in HIV and hepatitis C infections, by directly counting single molecules. Replacing fluorescent readout with a robust visual readout that can be captured by any unmodified cell phone camera will facilitate the global distribution of diagnostic tests, including in limited-resource settings where the need is greatest. This paper describes a methodology for developing a visual readout system for digital single-molecule amplification of RNA and DNA by (i) selecting colorimetric amplification-indicator dyes that are compatible with the spectral sensitivity of standard mobile phones, and (ii) identifying an optimal ratiometric image-process for a selected dye to achieve a readout that is robust to lighting conditions and camera hardware and provides unambiguous quantitative results, even for colorblind users. We also include an analysis of the limitations of this methodology, and provide a microfluidic approach that can be applied to expand dynamic range and improve reaction performance, allowing ultrasensitive, quantitative measurements at volumes as low as 5 nL. We validate this methodology using SlipChip-based digital single-molecule isothermal amplification with λDNA as a model and hepatitis C viral RNA as a clinically relevant target. The innovative combination of isothermal amplification chemistry in the presence of a judiciously chosen indicator dye and ratiometric image processing with SlipChip technology allowed the sequence-specific visual readout of single nucleic acid molecules in nanoliter volumes with an unmodified cell phone camera. When paired with devices that integrate sample preparation and nucleic acid amplification, this hardware-agnostic approach will increase the affordability and the distribution of quantitative diagnostic and environmental tests

Flanking Residues Are Central to DO11.10 T Cell Hybridoma Stimulation by Ovalbumin 323–339

Benjamin M. Roy is with UT Austin and University of Minnesota; Dmitriy V. Zhukov is with UT Austin; Jennifer A. Maynard is with UT Austin.T cell activation requires formation of a tri-molecular interaction between a major histocompatibility complex (MHC), peptide, and T cell receptor. In a common model system, the ovalbumin epitope 323–339 binds the murine class II MHC, I-Ad, in at least three distinct registers. The DO11.10 T cell recognizes the least stable of these, as determined by peptide-MHC dissociation rates. Using exogenous peptides and peptide insertions into a carrier protein in combination with IL-2 secretion assays, we show that the alternate registers do not competitively inhibit display of the active register four. In contrast, this weakly binding register is stabilized by the presence of N-terminal flanking residues active in MHC binding. The DO11.10 hybridoma is sensitive to the presence of specific wild-type residues extending to at least the P-3 peptide position. Transfer of the P-4 to P-2 flanking residues to a hen egg lysozyme epitope also presented by I-Ad increases the activity of that epitope substantially. These results illustrate the inherent complexity in delineating the interaction of multiple registers based on traditional thermodynamic measurements and demonstrate the potential of flanking residue modification for increasing the activity of weakly bound epitopes. The latter technique represents an alternative to substitution of anchor residues within a weakly bound register, which we show can significantly decrease the activity of the epitope to a responding T cell.Funding for this project was provided by the Packard Foundation, NSF DBI-0964137 and NIH 1R01GM095638 to JAM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Chemical Engineerin

Increasing Storage Battery Lifetime in Autonomous Photovoltaic Systems with Power Generation Structure Varying Throughout the Year

This paper substantiates the use of photovoltaic systems with power generation structure varying throughout the year. This research topic emerged from an in-depth analysis of the operating modes of autonomous photovoltaic systems located in Siberia and the Russian Far East. The paper gives a detailed and concise description of a methodology for modelling such a system with account of issues relating to the operational sustainability of diesel and solar power stations in autumn and winter. In spring and summer, autonomous photovoltaic systems operate using the standard power accumulation algorithm whereas the diesel power station serves as a stand-by power source thereby increasing the lifetime of storage batteries, reducing the number of their replacements and cutting down costs through discounting. The overall levelized cost of energy drops off significantly too. The paper presents the results of modelling an actual autonomous energy system in which a solar power station equipped with storage batteries is planned to be constructed in the near future. The modelling results revealed that using a structure varying throughout the year increases storage battery lifetime from 6 to 11 years, and there is only one (instead of three) replacement throughout the life of the batteries. The obtained results have been taken into consideration and are to be put into practice in setting up the photovoltaic system under review. The presented approach is versatile and can be used to analyze various photovoltaic systems

Sequences and activities of HEL peptide variants.

<p>EC₅₀ and maximum response values from 3-parameter curve fits of aggregate data from multiple (at least two) experiments.</p>*<p>p<0.01 by extra sum of squares f-test of curve fits for antigen vs. control (HEL11–25 for HEL peptides). Comparisons performed only on data from assays in which both antigens were tested (minimum of two independent assays).</p

H2-DMα is not responsible for the different activities of endogenously processed peptide variants.

<p>DO11.10 hybridoma and 3A5 antigen presenting cells containing mutant H2-DMα gene, were incubated overnight in the presence of <i>malE</i> chimeras containing ovalbumin epitope variants, followed by quantification of IL-2 release as a measure of T cell activation. <b><i>A</i></b><b>,</b> To assess the effects of removing alternate register anchor positions, truncated ovalbumin peptide inserts 325–337 (), 327–337 (), and 328–337 () were compared. <b><i>B</i></b><b>,</b> To assess the effect of stabilizing register three with P1 anchor substitutions, the control peptide 327–337 () was compared with variants 327 V(−2)M () and 327 V(−2)E (), substitutions which have been shown to confer enhanced I-A^d binding. Curve fits for the latter two are nearly identical, and lie atop one another. Data were fit to three-parameter curves with Graphpad Prism and are representative of two independent experiments; error bars show standard deviation of triplicate wells assayed for a given protein concentration.</p

Specific flanking residues but not alternate register stabilization enhances OVA peptide activity.

<p>DO11.10 hybridoma and antigen presenting cells were incubated overnight in the presence of exogenous peptide variants, followed by quantification of IL-2 released as a measure of T cell activation. <b><i>A</i></b><b>,</b> Wild-type ovalbumin 323–339 () was compared with peptide variants modified at anchor residues P4 (A to I) and P6 (I to V) in conjunction with additional changes in an effort to stabilize the active register four. Peptide variants include 327-339KIV () with an additional <i>n</i>-terminal truncation and P-2 modification (V to K) to prevent register shifting; 323-339EIVS () the full-length peptide with all four anchor residues altered to strongly binding residues; and 328-339EIVS, an <i>n</i>-terminal truncation of the previous variant (). The cell culture media contained 2 mM glutamine for this assay. <b><i>B</i></b><b>,</b> In a subsequent effort to stabilize register four by removing alternate register anchors, the wild-type 323–339 peptide () was compared with <i>n</i>-terminally truncated variants 325–337 (), 327–337 (), and 328–337 (). <b><i>C</i></b><b>,</b> To determine whether peptide length is responsible for the activity differences observed in the truncated variants, the 325–337 variant () which includes register four and the <i>n</i>-terminal P-1 to P-4 residues was compared with GGV328–337, in which the P-3 and P-4 positions were replaced with glycine () and a further truncated variant, 327–337 (), lacking the P-3 and P-4 residues. <b><i>D</i></b><b>,</b> To determine whether binding of register three enhances register four activity, we changed the register three P1 anchor residue (also register four P-2) to amino acids predicted to stabilize (M) or destabilize (S) register three. We compared three variants with identical length: variant GGV328–337 () with a wild-type V versus GGS328–337 () and GGM328–337 (). Data were fit to three-parameter curves with Graphpad Prism and are representative of three independent experiments; error bars show standard deviation of triplicate wells assayed for a given peptide concentration.</p

Sequences and activities of peptide variants in MalE carrier protein.

<p>EC₅₀ and maximum response values from 3-parameter curve fits of aggregate data from multiple (at least two) experiments. Positional numbering is in relation to the active register (register four in the case of OVA).</p>*<p>p<0.01 by extra sum of squares f-test of curve fits for antigen vs. control (MalE 327–337 for MalE chimeras). Comparisons performed only on data from assays in which both antigens were tested (minimum of two independent assays).</p

Cartoons depicting the tripartite interactions between the DO11.10 TCR, I-A^d MHC and the OVA 323–339 peptide in various registers.

<p><b><i>A</i></b>, The peptide is shown in register three, with the MHC anchor residues (P1, P4, P6 and P9) extending towards the MHC and residues interacting with the TCR (primarily P5 and to a lesser extent, P2 and P8) extending towards the TCR. <b><i>B</i></b><i>,</i> The peptide is shown in register four, with MHC anchor residues and TCR residues shown as above. The cartoon MHC has been modified to indicate potential interaction with flanking residues extending as far as P-4.</p