Functional un|unparsing

Danvy??s functional unparsing problem (Danvy in J. Funct. Program. 8(6), 621?C625, 1998) is to implement a type-safe ??printf?? function, which converts a sequence of heterogeneous arguments to a string according to a given format. The dual problem is to implement a type-safe ??scanf?? function, which extracts a sequence of heterogeneous arguments from a string by interpreting (Friedman and Wand in LFP, pp. 348?C355, 1984 and in Essentials of Programming Languages, MIT Press, 2008) the same format as an equally heterogeneous sequence of patterns that binds zero or more variables. We derive multiple solutions to both problems (Wand in J. ACM 27(1), 164?C180, 1980) from their formal specifications (Wand in Theor. Comput. Sci. 20(1), 3?C32, 1982). On one hand, our solutions show how the Hindley-Milner type system, unextended, permits accessing heterogeneous sequences with the static assurance of type safety. On the other hand, our solutions demonstrate the use of control operators (Felleisen et al. in Proceedings of the 1988 ACM Conference on Lisp and Functional Programming, pp. 52?C62, ACM Press, New York, 1988; Wand in POPL 85: Conference Record of the Annual ACM Symposium on Principles of Programming Languages, vol. 16, ACM Press, New York, 1985; Meyer and Wand in Logics of Programs, Lecture Notes in Computer Science, vol. 193, pp. 219?C224, Springer, Berlin, 1985) to communicate with formats as coroutines (Wand in Proceedings of the 1980 ACM Conference on Lisp and Functional Programming, vol. 12, pp. 285?C299, ACM Press, New York, 1980 and Haynes et al. in LFP, pp. 293?C298, 1984).     

Direct Method Based Control System for an Autonomous Quadrotor

This paper proposes a real time control algorithm for autonomous operation of a quadrotor unmanned air vehicle. The quadrotor is a small agile vehicle, which as well as being a excellent test bed for advanced control techniques could also be suitable for internal surveillance, search and rescue and remote inspection. The proposed control scheme incorporates two key aspects of autonomy; trajectory planning and trajectory following. Using the differentially-flat dynamics property of the system, the trajectory optimization is posed as a non-linear constrained optimization within the output space in the virtual domain, not explicitly related to the time domain. A suitable parameterization using a virtual argument as opposed to time is applied, which ensures initial and terminal constraint satisfaction. The speed profile is optimized independently, followed by the mapping to the time domain achieved using a speed factor. Trajectory following is achieved with a standard multi-variable control technique and a digital switch is used to re-optimize the reference trajectory in the event of infeasibility or mission change. The paper includes simulations using a full dynamic model of the quadrotor demonstrating the suitability of the proposed control scheme.     

DNA immobilization and SAW response in ZnO nanotips grown on LiNbO3 substrates.

DNA immobilization enhancement is demonstrated in a structure consisting of ZnO nanotips on 128 degrees Y-cut LiNbO3. The ZnO nanotips are grown by metalorganic chemical vapor deposition (MOCVD) on the top of a SiO2 layer that is deposited and patterned on the LiNbO3 SAW delay path. The effects of ZnO nanotips on the SAW response are investigated. X-ray diffraction and scanning electron microscopy are used to analyze the ZnO nanotips, which are of single crystalline quality, and they are uniformly aligned with their c-axis perpendicular to the substrate surface. The photoluminescence (PL) spectrum of the ZnO nanotips shows strong near bandedge transition with insignificant deep level emission, confirming their good optical property. DNA immobilization enhancement is experimentally validated by radioactive labeling tests and SAW response changes. The ZnO nanotips enhance the DNA immobilization by a factor of 200 compared to ZnO film with flat surface. DNA hybridization with complementary and noncomplementary second strand DNA oligonucleotides is used to study the selective binding of the structure. This device structure possesses the advantages of both traditional SAW sensors and ZnO nanostructures.     

Heavy-ion-induced luminescence of amorphous SiO2 during nanoparticle formation

Silica glass was implanted with negative 60 keV Cu ions at an ion flux from 5 to 75 μA/cm² up to a fluence of 1 × 10¹⁷ ions/cm² at initial sample temperatures of 300, 573 and 773 K. Spectra of ion-induced photon emission (IIPE) were collected in situ in the range from 250 to 850 nm. Optical absorption spectra of implanted specimens were ex situ measured in the range from 190 to 2500 nm.

IIPE spectra showed a broad band centered around 560 nm (2.2 eV) that was assigned to Cu⁺ solutes. The band appeared at the onset of irradiation, increased in intensity up to a fluence of about 5 × 10¹⁵ ions/cm² and then gradually decreased indicating three stage of the ion beam synthesis of nanoclusters: accumulation of implants, nucleation and growth nanoclusters. The IIPE intensity normalized on the ion flux is independent on the ion flux below 20 μA/cm²at higher fluences. The intensity of the band increased with increasing samples temperature, when optical absorption spectra reveal the increase of Cu nanoparticles size.     

Java-MaC: A Run-Time Assurance Approach for Java Programs

We describe Java-MaC, a prototype implementation of the Monitoring and Checking (MaC) architecture for Java programs. The MaC architecture provides assurance that the target program is running correctly with respect to a formal requirements specification by monitoring and checking the execution of the target program at run-time. MaC bridges the gap between formal verification, which ensures the correctness of a design rather than an implementation, and testing, which does not provide formal guarantees about the correctness of the system.Use of formal requirement specifications in run-time monitoring and checking is the salient aspect of the MaC architecture. MaC is a lightweight formal method solution which works as a viable complement to the current heavyweight formal methods. In addition, analysis processes of the architecture including instrumentation of the target program, monitoring, and checking are performed fully automatically without human direction, which increases the accuracy of the analysis. Another important feature of the architecture is the clear separation between monitoring implementation-dependent low-level behaviors and checking high-level behaviors, which allows the reuse of a high-level requirement specification even when the target program implementation changes. Furthermore, this separation makes the architecture modular and allows the flexibility of incorporating third party tools into the architecture. The paper presents an overview of the MaC architecture and a prototype implementation Java-MaC.     

High-Mobility Naphthalene Diimide Derivatives Revealed by Raman-Based In Silico Screening

Charge transport in crystalline organic semiconductors (OSCs) is considerably hindered by low-frequency vibrations introducing dynamic disorder in the charge transfer integrals. Recently, we have shown that the contributions of various vibrational modes to the dynamic disorder correlate with their Raman intensities and suggested a Raman-based approach for estimation of the dynamic disorder and search for potentially high-mobility OSCs. In the present paper, we showcase this approach by revealing the highest-mobility OSC(s) in two series of crystalline naphthalene diimide derivatives bearing alkyl or cycloalkyl substituents. In contrast to our previous studies, Raman spectra are not measured, but are instead calculated using periodic DFT. As a result, an OSC with a potentially high charge mobility is revealed in each of the two series, and further mobility calculations corroborate this choice. Namely, for the naphthalene diimide derivatives with butyl and cyclopentyl substituents, the estimated room-temperature isotropic electron mobilities are as high as 6 and 15 cm² V^–1 s^–1, respectively, in the latter case even exceeding 20 cm² V^–1 s^–1 in a two-dimensional plane. Thus, our results highlight the potential of using the calculated Raman spectra to search for high-mobility crystalline OSCs and reveal two promising OSCs, which were previously overlooked.     

Activation of Neutrophils by Mucin–Vaterite Microparticles

Nano- and microparticles enter the body through the respiratory airways and the digestive system, or form as biominerals in the gall bladder, salivary glands, urinary bladder, kidney, or diabetic pancreas. Calcium, magnesium, and phosphate ions can precipitate from biological fluids in the presence of mucin as hybrid nanoparticles. Calcium carbonate nanocrystallites also trap mucin and are assembled into hybrid microparticles. Both mucin and calcium carbonate polymorphs (calcite, aragonite, and vaterite) are known to be components of such biominerals as gallstones which provoke inflammatory reactions. Our study was aimed at evaluation of neutrophil activation by hybrid vaterite–mucin microparticles (CCM). Vaterite microparticles (CC) and CCM were prepared under standard conditions. The diameter of CC and CCM was 3.3 ± 0.8 µm and 5.8 ± 0.7 µm, with ƺ-potentials of −1 ± 1 mV and −7 ± 1 mV, respectively. CC microparticles injured less than 2% of erythrocytes in 2 h at 1.5 mg mL⁻¹, and no hemolysis was detected with CCM; this let us exclude direct damage of cellular membranes by microparticles. Activation of neutrophils was analyzed by luminol- and lucigenin-dependent chemiluminescence (Lum-CL and Luc-CL), by cytokine gene expression (IL-6, IL-8, IL-10) and release (IL-1β, IL-6, IL-8, IL-10, TNF-α), and by light microscopy of stained smears. There was a 10-fold and higher increase in the amplitude of Lum-CL and Luc-CL after stimulation of neutrophils with CCM relative to CC. Adsorption of mucin onto prefabricated CC microparticles also contributed to activation of neutrophil CL, unlike mucin adsorption onto yeast cell walls (zymosan); adsorbed mucin partially suppressed zymosan-stimulated production of oxidants by neutrophils. Preliminary treatment of CCM with 0.1–10 mM NaOCl decreased subsequent activation of Lum-CL and Luc-CL of neutrophils depending on the used NaOCl concentration, presumably because of the surface mucin oxidation. Based on the results of ELISA, incubation of neutrophils with CCM downregulated IL-6 production but upregulated that of IL-8. IL-6 and IL-8 gene expression in neutrophils was not affected by CC or CCM according to RT²-PCR data, which means that post-translational regulation was involved. Light microscopy revealed adhesion of CC and CCM microparticles onto the neutrophils; CCM increased neutrophil aggregation with a tendency to form neutrophil extracellular traps (NETs). We came to the conclusion that the main features of neutrophil reaction to mucin–vaterite hybrid microparticles are increased oxidant production, cell aggregation, and NET-like structure formation, but without significant cytokine release (except for IL-8). This effect of mucin is not anion-specific since particles of powdered kidney stone (mainly calcium oxalate) in the present study or calcium phosphate nanowires in our previous report also activated Lum-CL and Luc-CL response of neutrophils after mucin sorption.     

Sperm of Fruit Fly Drosophila melanogaster under Space Flight

Studies of reproductive function under long-term space flight conditions are of interest in planning the exploration of deep space. Motility, including the use of various inhibitors, cellular respiration, and the content of cytoskeletal proteins were studied, assessing the level of expression of the corresponding genes in spermatozoa of Drosophila melanogaster, which were in space flight conditions for 12 days. The experiment was carried out twice on board the Russian Segment of the International Space Station. Sperm motility speed after space flight, and subsequently 16 h after landing, is reduced relative to the control by 20% (p < 0.05). In comparison with the simulation experiment, we showed that this occurs as a result of the action of overloads and readaptation to the Earth’s gravity. At the same time, cellular respiration, the content of proteins of the respiratory chain, and the expression of their genes do not change. We used kinase inhibitor 6-(dimethylamino)purine (6-DMAP) and phosphatase inhibitors; 6-DMAP restored the reduced the speed of spermatozoa in the flight group to that of the control. These results can be useful in developing a strategy for protecting reproductive health during the development of other bodies in the solar system.     

Toxicity of Different Types of Surfactants via Cellular and Enzymatic Assay Systems

Surfactants have a widespread occurrence, not only as household detergents, but also in their application in industry and medicine. There are numerous bioassays for assessing surfactant toxicity, but investigations of their impact on biological systems at the molecular level are still needed. In this paper, luminous marine bacteria and their coupled NAD(P)H:FMN-oxidoreductase + luciferase (Red + Luc) enzyme system was applied to examine the effects of different types of surfactants, including cationic cetyltrimethylammonium bromide (CTAB), non-ionic polyoxyethylene 20 sorbitan monooleate (Tween 80) and anionic sodium lauryl sulfate (SLS), and to assess whether the Red + Luc enzyme system can be used as a more sensitive indicator of toxicity. It was shown that the greatest inhibitory effect of the surfactants on the activity of luminous bacteria and the Red + Luc enzyme system was in the presence of SLS samples. The calculated IC₅₀ and EC₅₀ values of SLS were 10⁻⁵ M and 10⁻² M for the enzymatic and cellular assay systems, respectively. The results highlight the benefits of using the enzymatic assay system in ecotoxicology as a tool for revealing surfactant effects on intracellular proteins if the cellular membrane is damaged under a long-term exposure period in the presence of the surfactants. For this purpose, the bioluminescent enzyme-inhibition-based assay could be used as an advanced research tool for the evaluation of surfactant toxicity at the molecular level of living organisms due to its technical simplicity and rapid response time.     

Microsatellite Instability in Russian Patients with Colorectal Cancer

The aim of this study was to determine the characteristics of Russian patients with microsatellite instability (MSI) tumors. MSI in the tumor was determined in 514 patients with colon cancer using PCR and subsequent fragment analysis for five markers (NR21, NR24, BAT25, BAT26, and NR27). In the presence of microsatellite instability, the mismatch repair (MMR) system genes were examined using the NGS and MLPA methods to establish the diagnosis of Lynch syndrome. The overall frequency of MSI tumors was 15%: at stage I—19% (9/48), at stage II—21% (44/213), at stage III—16% (26/160), and at stage IV—2% (2/93). Patients with MSI tumors differed in the age of diagnosis, tumor localization, time of cancer recurrence, and stage of the disease. The overall and disease-free survival of patients whose tumors had MSI status was higher than that of patients with microsatellite-stable status, p = 0.04 and p = 0.02, respectively. Analysis of overall and disease-free survival of patients with Lynch syndrome and patients with sporadic colon cancer, but with MSI status, did not reveal significant differences, p = 0.52 and p = 0.24, respectively. The age of patients with Lynch syndrome was significantly younger than that of patients with sporadic colon cancer whose tumors had MSI status (p < 0.001).