Derivation of nearest-neighbor DNA parameters in magnesium from single-molecule experiments

DNA hybridization is an essential molecular reaction in biology with many applications. The nearest-neighbor (NN) model for nucleic acids predicts DNA thermodynamics using energy values for the different base pair motifs. These values have been derived from melting experiments in monovalent and divalent salt and applied to predict melting temperatures of oligos within a few degrees. However, an improved determination of the NN energy values and their salt dependencies in magnesium is still needed for current biotechnological applications seeking high selectivity in the hybridization of synthetic DNAs. We developed a methodology based on single molecule unzipping experiments to derive accurate NN energy values and initiation factors for DNA. A new set of values in magnesium is derived, which reproduces unzipping data and improves melting temperature predictions for all available oligo lengths, in a range of temperature and salt conditions where correlation effects between the magnesium bound ions are weak. The NN salt correction parameters are shown to correlate to the GC content of the NN motifs. Our study shows the power of single-molecule force spectroscopy assays to unravel novel features of nucleic acids such as sequence-dependent salt corrections

The effect of sintering temperature on the properties of the BiOCl films for potential application in DSSC

In this work, BiOCl films were obtained by tape casting using BiOCl powders synthesized by the co-precipitation method. The effect of the film's sintering temperature (300 °C–600 °C) on the morphology, chemical composition, crystalline phases and optical characteristics was studied. The obtained BiOCl powders showed a flake-like morphology, a tetragonal crystalline structure without secondary phases and a wide band gap of 3.53 eV. For BiOCl films, results indicated that as the sintering temperature increased the flake-like shaped particles changed to rectangular ones while the amount of chlorine in the films decreased. A phase transition from tetragonal BiOCl to monoclinic Bi24O31Cl10 was also observed as the sintering temperature increased. Consequently, optical studies revealed that the band gap of BiOCl films decreased from 3.03 eV to 2.82 eV. FTIR analysis demonstrated that the organic groups were removed from the films only for sintering temperatures above 400 °C. The Rhodamine B dye adsorption capacity of BiOCl films decreased with increasing sintering temperature. The results obtained allow us to conclude that BiOCl films are suitable for use in DSSC when the sintering temperature is in the range of 400–500 °C

Interleaved Sequence RNNs for Fraud Detection

Payment card fraud causes multibillion dollar losses for banks and merchants worldwide, often fueling complex criminal activities. To address this, many real-time fraud detection systems use tree-based models, demanding complex feature engineering systems to efficiently enrich transactions with historical data while complying with millisecond-level latencies. In this work, we do not require those expensive features by using recurrent neural networks and treating payments as an interleaved sequence, where the history of each card is an unbounded, irregular sub-sequence. We present a complete RNN framework to detect fraud in real-time, proposing an efficient ML pipeline from preprocessing to deployment. We show that these feature-free, multi-sequence RNNs outperform state-of-the-art models saving millions of dollars in fraud detection and using fewer computational resources.Comment: 9 pages, 4 figures, to appear in SIGKDD'20 Industry Trac

Lightweight Automated Feature Monitoring for Data Streams

Monitoring the behavior of automated real-time stream processing systems has become one of the most relevant problems in real world applications. Such systems have grown in complexity relying heavily on high dimensional input data, and data hungry Machine Learning (ML) algorithms. We propose a flexible system, Feature Monitoring (FM), that detects data drifts in such data sets, with a small and constant memory footprint and a small computational cost in streaming applications. The method is based on a multi-variate statistical test and is data driven by design (full reference distributions are estimated from the data). It monitors all features that are used by the system, while providing an interpretable features ranking whenever an alarm occurs (to aid in root cause analysis). The computational and memory lightness of the system results from the use of Exponential Moving Histograms. In our experimental study, we analyze the system's behavior with its parameters and, more importantly, show examples where it detects problems that are not directly related to a single feature. This illustrates how FM eliminates the need to add custom signals to detect specific types of problems and that monitoring the available space of features is often enough.Comment: 10 pages, 5 figures. AutoML, KDD22, August 14-17, 2022, Washington, DC, U

Sistema de detección de tránsito vehicular

La tecnología de detección de tráfico vehicular ha demostrado ser un área de diseño avanzada, capaz de lograr mejoras sustanciales en un rango de aplicaciones debido a su paradigma de la estructura de toma de decisiones basado en el razonamiento cognitivo. El presente trabajo presenta el desarrollo de un avance en la tecnología de detección vehicular que permite incluir un modelo formal basado en un agente autónomo e inteligente capaz de detectar vehículos a través de un solo sensor, de acuerdo a las exigencias y limitaciones de las avenidas. Se utilizaron los periféricos de UART (Universal Asynchronous Receiver-Transmiter), RTC (Real Time Clock), DMA (Direct Memory Access), para el manejo de los datos, así como una aplicación como interfaz de usuario para mostrar la cantidad de tránsito. Este proceso mejora efectiva e inmediatamente la calidad del servicio en una intersección, aumentando el rendimiento de la movilidad de los vehículos. Este prototipo tiene como ventaja no solo la mejora en tiempo de traslados, sino que también el costo de producción. Se realizaron una serie de pruebas en campo con el fin de comparar la funcionalidad, ventajas y desventajas sobre otros sistemas de detección ya creados, con la intención de alcanzar un control de tránsito más barato y eficiente.Consejo Nacional de Ciencia y Tecnologí

Dynamic force spectroscopy of DNA hairpins. I. Force kinetics and free energy landscapes

We investigate the thermodynamics and kinetics of DNA hairpins that fold/unfold under the action of applied mechanical force. We introduce the concept of the molecular free energy landscape and derive simplified expressions for the force dependent Kramers-Bell rates. To test the theory we have designed a specific DNA hairpin sequence that shows two-state cooperative folding under mechanical tension and carried out pulling experiments using optical tweezers. We show how we can determine the parameters that characterize the molecular free energy landscape of such sequence from rupture force kinetic studies. Finally we combine such kinetic studies with experimental investigations of the Crooks fluctuation relation to derive the free energy of formation of the hairpin at zero force.Comment: 28 pages, 12 figure

The Wigner function associated to the Rogers-Szego polynomials

We show here that besides the well known Hermite polynomials, the q-deformed harmonic oscillator algebra admits another function space associated to a particular family of q-polynomials, namely the Rogers-Szego polynomials. Their main properties are presented, the associated Wigner function is calculated and its properties are discussed. It is shown that the angle probability density obtained from the Wigner function is a well-behaved function defined in the interval [-Pi,Pi), while the action probability only assumes integer values greater or equal than zero. It is emphasized the fact that the width of the angle probability density is governed by the free parameter q characterizing the polynomial.Comment: 12 pages, 2 (mathemathica) figure

Synthesis of BiOI/Mordenite Composites for Photocatalytic Treatment of Organic Pollutants Present in Agro-Industrial Wastewater

Recently, bismuth oxyiodide (BiOI) is an attractive semiconductor to use in heterogeneous photocatalysis processes. Unfortunately, BiOI individually shows limited photocatalytic efficiency, instability, and a quick recombination of electron/holes. Considering the practical application of this semiconductor, some studies show that synthetic zeolites provide good support for this photocatalyst. This support material permits a better photocatalytic efficiency because it prevents the quick recombination of photogenerated pairs. However, the optimal conditions (time and temperature) to obtain composites (BiOI/ synthetic zeolite) with high photocatalytic efficiency using a coprecipitation-solvothermal growth method have not yet been reported. In this study, a response surface methodology (RSM) based on a central composite design (CCD) was applied to optimize the synthesis conditions of BiOI/mordenite composites. For this purpose, eleven BiOI/mordenite composites were synthesized using a combined coprecipitation-solvothermal method under different time and temperature conditions. The photocatalytic activities of the synthesized composites were evaluated after 20 min of photocatalytic oxidation of caffeic acid, a typical organic pollutant found in agro-industrial wastewater. Moreover, BiOI/mordenite composites with the highest and lowest photocatalytic activity were physically and chemically characterized using nitrogen adsorption isotherms, scanning electron microscopy (SEM), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), and diffuse reflectance spectroscopy (DRS). The optimal synthesis conditions prove to be 187 °C and 9 h. In addition, the changes applied to the experimental conditions led to surface property modifications that influenced the photocatalytic degradation efficiency of the BiOI/mordenite composite toward caffeic acid photodegradation

Performance deficits of NK1 receptor knockout mice in the 5 choice serial reaction time task: effects of d Amphetamine, stress and time of day.

Background The neurochemical status and hyperactivity of mice lacking functional substance P-preferring NK1 receptors (NK1R-/-) resemble abnormalities in Attention Deficit Hyperactivity Disorder (ADHD). Here we tested whether NK1R-/- mice express other core features of ADHD (impulsivity and inattentiveness) and, if so, whether they are diminished by d-amphetamine, as in ADHD. Prompted by evidence that circadian rhythms are disrupted in ADHD, we also compared the performance of mice that were trained and tested in the morning or afternoon. Methods and Results The 5-Choice Serial Reaction-Time Task (5-CSRTT) was used to evaluate the cognitive performance of NK1R-/- mice and their wildtypes. After training, animals were tested using a long (LITI) and a variable (VITI) inter-trial interval: these tests were carried out with, and without, d-amphetamine pretreatment (0.3 or 1 mg/kg i.p.). NK1R-/- mice expressed greater omissions (inattentiveness), perseveration and premature responses (impulsivity) in the 5-CSRTT. In NK1R-/- mice, perseveration in the LITI was increased by injection-stress but reduced by d-amphetamine. Omissions by NK1R-/- mice in the VITI were unaffected by d-amphetamine, but premature responses were exacerbated by this psychostimulant. Omissions in the VITI were higher, overall, in the morning than the afternoon but, in the LITI, premature responses of NK1R-/- mice were higher in the afternoon than the morning. Conclusion In addition to locomotor hyperactivity, NK1R-/- mice express inattentiveness, perseveration and impulsivity in the 5-CSRTT, thereby matching core criteria for a model of ADHD. Because d-amphetamine reduced perseveration in NK1R-/- mice, this action does not require functional NK1R. However, the lack of any improvement of omissions and premature responses in NK1R-/- mice given d-amphetamine suggests that beneficial effects of this psychostimulant in other rodent models, and ADHD patients, need functional NK1R. Finally, our results reveal experimental variables (stimulus parameters, stress and time of day) that could influence translational studies

Single-molecule derivation of salt dependent base-pair free energies in DNA

Accurate knowledge of the thermodynamic properties of nucleic acids is crucial to predicting their structure and stability. To date most measurements of base-pair free energies in DNA are obtained in thermal denaturation experiments, which depend on several assumptions. Here we report measurements of the DNA base-pair free energies based on a simplified system, the mechanical unzipping of single DNA molecules. By combining experimental data with a physical model and an optimization algorithm for analysis, we measure the 10 unique nearest-neighbor base-pair free energies with 0.1 kcal mol-1 precision over two orders of magnitude of monovalent salt concentration. We find an improved set of standard energy values compared with Unified Oligonucleotide energies and a unique set of 10 base-pair-specific salt-correction values. The latter are found to be strongest for AA/TT and weakest for CC/GG. Our new energy values and salt corrections improve predictions of DNA unzipping forces and are fully compatible with melting temperatures for oligos. The method should make it possible to obtain free energies, enthalpies and entropies in conditions not accessible by bulk methodologies.Comment: Main text: 27 pages, 4 figures, 2 tables. Supporting Information: 51 pages, 19 figures, 4 table