BINA

Single Nucleotide Polymorphism markers (SNPs) have great potential to identify individuals, family relations, biogeographical ancestry, and phenotypic traits. In many forensic situations DNA mixtures of a victim and an unknown suspect exist. Extracting from such samples the suspect's SNP profile can be used to assist investigation and gather intelligence. Computational tools to determine inclusion/exclusion of a known individual from a mixture exist, but no algorithm to extract an unknown SNP profile without a list of suspects is available. We present here AH-HA, a novel computational approach for extracting an unknown SNP profile from a whole genome sequencing (WGS) of a two person mixture. It utilizes techniques similar to the ones used in haplotype phasing. It constructs the inferred genotype as an imperfect mosaic of haplotypes from a reference panel of the target population. It is shown to outperform more simplistic approaches, maintaining high performance through a wide range of sequencing depths (500x-5x). AH-HA can be applied in cases of victim-suspect mixtures and improve the capabilities of the investigating forces. This approach can be extended to more complex mixtures, with more donors and less prior information, further motivating the development of SNP based forensics technologies.

In recent years, lignin has drawn increasing attention for different applications due to its intrinsic antibacterial and antioxidant properties, coupled with biodegradability and biocompatibility. However, chemical modification or combination with metals is usually required to increase its antimicrobial functionality and produce biobased added-value materials for applications wherein bacterial growth should be avoided, such as biomedical and food industries. In this work, a sonoenzymatic approach for the simultaneous functionalization and nanotransformation of lignin to prepare metal-free antibacterial phenolated lignin nanoparticles (PheLigNPs) is developed. The grafting of tannic acid, a natural phenolic compound, onto lignin was achieved by an environmentally friendly approach using laccase oxidation upon the application of high-intensity ultrasound to rearrange lignin into NPs. PheLigNPs presented higher …

Solid-state batteries have received renewed attention in recent years. The present study compares all-solid-state sodium batteries containing polyethylene oxide (PEO) polymer electrolyte (PE) with two salts, NaPF6 and NaClO4. Electrochemical properties were determined by means of both AC and DC measurements. Battery prototypes with PEO:NaClO4 have a better specific capacity; however, a composite electrolyte system containing TiO2 nanoparticles shows greater influence in PEO:NaPF6. This is probably due to the titania particles acting as a scavenger of HF, an inevitable contaminant in electrolyte systems containing PF6- anions.

Performance, durability, and abundance/cost of electrocatalytic materials are fundamental parameters in for large electrochemical storage solutions like redox-flow batteries (RFB). The acidic environment in Hydrogen–Bromine RFB (HBRFB), which targets tens of thousands of hours in durability, makes the challenge even more acute. Continuous effort to find the most effective and stable catalyst can promote HBRFB goal to become sustainable for high power storage systems. Herein, we explore the lower limits in catalyst loading for the two most active precious group metals (PGMs) – platinum and iridium (individually and in a bimetallic catalyst). The catalyst has been structurally characterized and lab-scale redox-flow cells have been cycled with a decreasing loading of PGM. Carbon support and polymeric coating on Pt catalyst shows a significant increase in the utilization of the catalyst. It enables low platinum …

Nuclear speckles are dynamic membraneless bodies located in the cell nucleus. They harbor RNAs and proteins, many of which are splicing factors, that together display complex biophysical properties dictating nuclear speckle formation and maintenance. Although these nuclear bodies were discovered decades ago, only recently has in-depth genomic analysis begun to unravel their essential functions in modulation of gene activity. Major advancements in genomic mapping techniques combined with microscopy approaches have enabled insights into the roles nuclear speckles may play in enhancing gene expression, and how gene positioning to specific nuclear landmarks can regulate gene expression and RNA processing. Some studies have drawn a link between nuclear speckles and disease. Certain maladies either involve nuclear speckles directly or dictate the localization and reorganization of many nuclear speckle factors. This is most striking during viral infection, as viruses alter the entire nuclear architecture and highjack host machinery. As discussed in this Review, nuclear speckles represent a fascinating target of study not only to reveal the links between gene positioning, genome subcompartments and gene activity, but also as a potential target for therapeutics.

Cascades are self-amplifying processes triggered by feedback mechanisms that may cause a substantial part of a macroscopic system to change its phase in response of a relatively small local event. The theoretical background for these phenomena is rich and interdisciplinary with interdependent networks providing a versatile "two-interactions" framework to study their multiscale evolution. Yet, physics experiments aimed at validating this ever-growing volume of predictions have remained elusive, hitherto hindered by the problem of identifying possible physical mechanisms realizing interdependent couplings. Here we develop and study the first experimental realization of an interdependent system as a multilayer network of two disordered superconductors separated by an insulating film. We show that Joule heating effects emerging at sufficiently large driving currents act as dependency links between the superconducting layers, igniting overheating cascades via adaptive back and forth electro-thermal feedbacks. Through theory and experiments, we unveil a rich phase diagram of mutual resistive transitions and cascading processes that physically realize and generalize interdependent percolation. The present work establishes the first physics laboratory bench for the manifestation of the theory of interdependent systems, enabling experimental studies to control and to further develop the multilayer phenomena of complex interdependent materials.

Variation of grating amplitudes on a surface of amorphous chalcogenide films (ACF) As20Se80 has been studied under illumination by a band-gap light with the purpose to understand mechanism of photo-induced (PI) mass transfer. After holographic recording of surface relief gratings (SRGs) of various periods Λ (from 3 to 15 µm) they were illuminated by a diode laser (λ = 660 nm) and their profile variation was analyzed using optical microscopy, atomic force microscopy, light scattering, and optical profilometry. The SRGs with Λ < 8 µm exponentially flattened with time of illumination, whereas amplitudes of the SRGs with Λ > 8 µm exponentially grew. Theoretical analysis of the kinetics of PI mass transfer shows that the SRG profile variation occurs by bulk diffusion of As and Se atoms as a result of competition between capillary forces and electrostatic forces created by redistribution of electrons and holes generated …

We perform numerical studies of a thermally driven, overdamped particle in a random quenched force field, known as the Sinai model. We compare the unbounded motion on an infinite 1-dimensional domain to the motion in bounded domains with reflecting boundaries and show that the unbounded motion is at every time close to the equilibrium state of a finite system of growing size. This is due to time scale separation: Inside wells of the random potential, there is relatively fast equilibration, while the motion across major potential barriers is ultraslow. Quantities studied by us are the time dependent mean squared displacement, the time dependent mean energy of an ensemble of particles, and the time dependent entropy of the probability distribution. Using a very fast numerical algorithm, we can explore times up top steps and thereby also study finite-time crossover phenomena.

Developing high performance, cost-effective, and durable electrocatalysts that must be derived from non-noble metals is crucial for alkaline oxygen evolution reaction (OER). OER, which takes place at the anode, is accepted as a major obstacle for commercialization due to its sluggish kinetics. In this study, a two-step synthesis method, such as a hydrothermal process followed by the annealing of the reactants in an Ar-filled Swagelok cell, is briefly described to obtain a cubic type of Co3O4 core and CoP shell. As a result of synergy, Co3O4 vertical bar CoP demonstrates an onset overpotential of 280 mV and reaches a current density of 10 mA cm(-2) at an overpotential of 320 mV in an alkaline medium (pH = 13.5). The electronic property of the heterojunction is verified by the Tauc plot and valence band XPS. The band structure indicates that Co3O4 vertical bar CoP exhibits a more metallic character than pristine …

Developing high performance, cost-effective, and durable electrocatalysts that must be derived from non-noble metals is crucial for alkaline oxygen evolution reaction (OER). OER, which takes place at the anode, is accepted as a major obstacle for commercialization due to its sluggish kinetics. In this study, a two-step synthesis method, such as a hydrothermal process followed by the annealing of the reactants in an Ar-filled Swagelok cell, is briefly described to obtain a cubic type of Co3O4 core and CoP shell. As a result of synergy, Co3O4|CoP demonstrates an onset overpotential of 280 mV and reaches a current density of 10 mA cm–2 at an overpotential of 320 mV in an alkaline medium (pH = 13.5). The electronic property of the heterojunction is verified by the Tauc plot and valence band XPS. The band structure indicates that Co3O4|CoP exhibits a more metallic character than pristine Co3O4 due to the fact that …

We demonstrate a novel method for focusing a probe IR pulse laser beam in semiconductors. The shaping was done by a temporaly modifying the material complex refractive index by a second pulse pump laser beam absorbed in the sample, using pump-prob experiment.

Integrated microwave photonic filters are becoming increasingly important for signal processing within advanced wireless and cellular networks. Filters with narrow transmission passbands mandate long time delays, which are difficult to accommodate within photonic circuits. Long delays may be obtained through slow moving acoustic waves instead. Input radio-frequency information can be converted from one optical carrier to another via surface acoustic waves and filtered in the process. However, the transfer functions of previously reported devices consisted of multiple periodic passbands, and the selection of a single transmission band was not possible. In this work, we demonstrate surface acoustic wave, silicon-photonic filters of microwave frequency with a single transmission passband. The filter response consists of up to 32 tap coefficients, and the transmission bandwidth is only 7 MHz. The results extend the capabilities of integrated microwave photonics in the standard silicon-on-insulator platform.

Fuel cells are already employed in commercial transportation even though their price is still too high to enable widespread production. A viable and promising pathway taken to lower this price is the replacement of expensive constitutes, namely the platinum-based catalysts at the cathode, by platinum group metal-free catalysts based on abundant materials, such as iron. This led to the development of iron-based catalysts that show high activity towards the oxygen reduction reaction. The extraction of the intrinsic catalytic activity of any catalyst is important both for finding relations between the chemical properties of the active sites and their activity, as well as a comparison measure between catalysts. An important parameter that has been elusive for many years is the turnover frequency, which is derived form the number of electrochemical active sites’ density (EASD). The ability to measure the EASD was very limited …

Recent research points to mesenchymal stem cells’ potential for treating neurological disorders, especially drug addiction. We examined the longitudinal effect of placenta-derived mesenchymal stromal-like cells (PLX-PAD) in a rat model for cocaine addiction. Sprague–Dawley male rats were trained to self-administer cocaine or saline daily until stable maintenance. Before the extinction phase, PLX-PAD cells were administered by intracerebroventricular or intranasal routes. Neurogenesis was evaluated, as was behavioral monitoring for craving. We labeled the PLX-PAD cells with gold nanoparticles and followed their longitudinal migration in the brain parallel to their infiltration of essential peripheral organs both by micro-CT and by inductively coupled plasma-optical emission spectrometry. Cell locations in the brain were confirmed by immunohistochemistry. We found that PLX-PAD cells attenuated cocaine-seeking behavior through their capacity to migrate to specific mesolimbic regions, homed on the parenchyma in the dentate gyrus of the hippocampus, and restored neurogenesis. We believe that intranasal cell therapy is a safe and effective approach to treating addiction and may offer a novel and efficient approach to rehabilitation.

In this paper, we present large-field, five-step lattice structured illumination microscopy (Lattice SIM). This method utilizes a 2D grating for lattice projection and a spatial light modulator (SLM) for phase shifting. Five phase-shifted intensity images are recorded to reconstruct a super-resolution image, enhancing the imaging speed and reducing the photo-bleaching both by 17%, compared to conventional two-direction and three-shift SIM. Furthermore, lattice SIM has a three-fold spatial bandwidth product (SBP) enhancement compared to SLM/DMD-based SIM, of which the fringe number is limited by the SLM/DMD pixel number. We believe that the proposed technique will be further developed and widely applied in many fields.

Gene expression measurements of tissues, tumors, or cell lines taken over multiple time points are valuable for describing dynamic biological phenomena such as the response to growth factors. However, such phenomena typically involve multiple biological processes occurring in parallel, making it difficult to identify and discern their respective contributions at any time point. Here, we demonstrate the use of unsupervised machine learning to deconvolve a series of time-dependent gene expression measurements into its underlying temporal components. We first downloaded publicly available RNAseq data obtained from synchronized HeLa cells at consecutive time points following release from cell cycle arrest. Then, we used Fourier analysis and Topic modeling to reveal three underlying components and their relative contributions at each time point. We identified two temporal components with oscillatory behavior, corresponding to the G1-S and G2-M phases of the cell cycle, and a third component with a transient expression pattern, associated with the immediate-early response gene program, regulation of cell proliferation, and cervical cancer. This study demonstrates the use of unsupervised machine learning to identify hidden temporal components in biological systems, with potential applications to early detection and monitoring of diseases and recovery processes.

We report persistent 100-fs period Rabi oscillations between 1s and 2p excitons in halide perovskite single crystals driven by off-resonant low-frequency phonon modes. This contrasts with prevailing models for the electron-phonon coupling in these materials.

Carbon aerogels have been studied in the context of fuel cell electrodes mainly as catalyst support materials due to their high surface area, porosity, and electrical conductivity. Recently, aerogels composed solely of inorganic molecular complexes have shown to be promising materials for the electrocatalysis of oxygen reduction reaction (ORR). These aerogels consist of atomically dispersed catalytic sites. Herein, we report on the synthesis and characterization of an aerogel-based catalyst: iron phthalocyanine aerogel. It was synthesized by coupling of ethynyl-terminated phthalocyanine monomers and then heat-treated at 800 °C to increase its electrical conductivity and catalytic activity. The aerogels reported here were tested as catalysts for ORR in acidic conditions for the first time and found to have a ultra-high number of atomically dispersed catalytic sites (7.11 × 1020 sites g–1) and very good catalytic activity (E …

The rising interest in polymer electrolyte fuel cell (PEFC) technology, part of the global shift in energy production to clean sources, is accompanied by efforts to drive down the cost of this technology, which focus primarily on the cathode catalyst, the most expensive PEFC component. While platinum-group metals (PGMs) continues to be the materials of choice for oxygen reduction reaction (ORR) catalysts, use of these materials in PEFCs must be significantly reduced or eliminated without a penalty in the overall cell performance for PEFC technology to become fully viable.The most promising class ORR catalysts that do not utilize PGMs (i.e., PGM-free catalysts), involve first-row transition metals, such as iron and cobalt incorporated in a nitrogen-doped carbon (M-N-C catalysts). While advancements in M-N-C activity have been impressive, the much sought-after improvement in durability has been impeded by limited …

Inherited retinal diseases (IRDs) are a clinically complex and heterogenous group of visual impairment phenotypes caused by pathogenic variants in at least 277 nuclear and mitochondrial genes, affecting different retinal regions, and depleting the vision of affected individuals. Genes that cause IRDs when mutated are unique by possessing differing genotype-phenotype correlations, varying inheritance patterns, hypomorphic alleles, and modifier genes thus complicating genetic interpretation. Next-generation sequencing has greatly advanced the identification of novel IRD-related genes and pathogenic variants in the last decade. For this review, we performed an in-depth literature search which allowed for compilation of the Global Retinal Inherited Disease (GRID) dataset containing 4,798 discrete variants and 17,299 alleles published in 31 papers, showing a wide range of frequencies and complexities among …