BINA

Trypanosoma brucei, the parasite that causes sleeping sickness, cycles between an insect and a mammalian host. However, the effect of RNA modifications such as pseudouridinylation on its ability to survive in these two different host environments is unclear. Here, two genome-wide approaches were applied for mapping pseudouridinylation sites (Ψs) on small nucleolar RNA (snoRNA), 7SL RNA, vault RNA, and tRNAs from T. brucei. We show using HydraPsiSeq and RiboMeth-seq that the Ψ on C/D snoRNA guiding 2′-O-methylation increased the efficiency of the guided modification on its target, rRNA. We found differential levels of Ψs on these noncoding RNAs in the two life stages (insect host and mammalian host) of the parasite. Furthermore, tRNA isoform abundance and Ψ modifications were characterized in these two life stages demonstrating stage-specific regulation. We conclude that the differential Ψ …

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 …

High-throughput scanning electron microscopy (SEM) coupled with classification using neural networks is an ideal method to determine the morphological handedness of large populations of chiral nanoparticles. Automated labeling removes the time-consuming manual labeling of training data, but introduces label error, and subsequently classification error in the trained neural network. Here, we evaluate methods to minimize classification error when training from automated labels of SEM datasets of chiral Tellurium nanoparticles. Using the mirror relationship between images of opposite handed particles, we artificially create populations of varying label error. We analyze the impact of label error rate and training method on the classification error of neural networks on an ideal dataset and on a practical dataset. Of the three training methods considered, we find that a pretraining approach yields the most accurate …

We study the effect of acoustic phonons on the quantum phase transition in the O (N) model. We develop a renormalization group (RG) analysis near (3+ 1) space-time dimensions and derive the RG equations using an ε expansion. Our results indicate that when the number of flavors of the underlying O (N) model exceeds a critical number N c= 4, the quantum transition remains second-order of the Wilson-Fisher type while, for N≤ 4, it is a weakly first-order transition. We characterize this weakly first-order transition by a length scale ξ*, below which the behavior appears to be critical. At finite temperatures for N≤ 4, a tricritical point separates the weakly first-order and second-order transitions.

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 …

Solid-state batteries have received renewed attention in recent years. The present study compares all-solid-state sodium batteries containing sodium metal anodes, NaTi 2 (PO 4) 3 (NTP) cathodes and PEO polymer electrolyte (PE) with two salts—NaPF 6 and NaClO 4. Electrochemical properties were determined by means of both AC and DC measurements. For fresh symmetric cells, it seems like using NaClO 4 as the salt leads to a lower interfacial resistance, but during contact with Na anodes, PEO: NaClO 4 PE produces an unstable interface whereas PEO-NaPF 6 forms a stable interface upon contact with sodium anodes. Battery prototypes with PEO: NaClO 4 showed a better performance than those using PEO: NaPF 6 in terms of specific capacity and energy content, as NaPF 6 produces HF by-product which impairs the performance of full cells. However, the use of composite solid electrolyte containing PEO …

Single-nucleotide polymorphism (SNP) markers 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 SNP profiles from suspect’s samples can be used to assist investigation or gather intelligence. Computational tools to determine inclusion/exclusion of a known individual from a mixture exist, but no algorithm for extraction of an unknown SNP profile without a list of suspects is available. Here, we present an advanced haplotype-based HMM algorithm (AH-HA), a novel computational approach for extracting an unknown SNP profile from whole genome sequencing (WGS) of a two-person mixture. AH-HA 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 outperforms more simplistic approaches, maintaining high performance through a wide range of sequencing depths (500×–5×). AH-HA can be applied in cases of victim–suspect mixtures and improves 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.

Single-nucleotide polymorphism (SNP) markers 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 SNP profiles from suspect’s samples can be used to assist investigation or gather intelligence. Computational tools to determine inclusion/exclusion of a known individual from a mixture exist, but no algorithm for extraction of an unknown SNP profile without a list of suspects is available. Here, we present an advanced haplotype-based HMM algorithm (AH-HA), a novel computational approach for extracting an unknown SNP profile from whole genome sequencing (WGS) of a two-person mixture. AH-HA 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 outperforms more simplistic approaches, maintaining high performance through a wide range of sequencing depths (500×–5×). AH-HA can be applied in cases of victim–suspect mixtures and improves 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.

The incompatibility of physical observables is one of the hallmarks of quantum mechanics. This form of non-classicality, encapsulated by negative quasiprobabilities, has been shown to underlie metrological and thermodynamical advantages and it can be related with information scrambling and dynamical phase transitions in many-body systems. In this work, we use a nitrogen-vacancy center in diamond to realize the experimental implementation of a weak two-point measurement scheme to reconstruct the Margenau-Hill quasiprobability distribution, whose negativity implies non-classicality. Finally, we experimentally show work extraction, empowered by non-classicality, beyond the classical case.

Chiral surfaces, developed in the last decade, serve as media for enantioselective chemical reactions. Until today, they have been based mostly on developments in silica templating, and are made mainly from imprints of silicate materials developed a long time ago. Here, a chiral porous activated carbon surface was developed based on a chiral ionic liquid, and the surface chemistry and pore structure were studied to lay a new course of action in the field. The enantioselectivities of surfaces are examined by using variety of methods such as circular dichroism, linear sweep voltammetry and catalysis. These techniques revealed a 28.1% preference for the D enantiomer of the amino acid proline, and linear sweep voltammetry confirmed chirality recognition by another probe. An aldol surface chiral catalytic reaction was devised and allowed to determine the root of the enantiomeric excess. These results affirm the path toward a new type of chiral surface.

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.

Adsorbed surface ligands play an important role in determining the chemical and physical properties of colloidal semiconductor nanocrystals. Most particularly, these ligands influence the optical properties of these nanocrystals. For instance, the luminescence of type II–VI quantum dots has been shown to decrease as metal carboxylates are stripped from the surface. To gain a better understanding of the thermodynamics and equilibria that influence the optical properties of colloidal quantum dots, we studied the adsorption energies of aliphatic cadmium carboxylates to the surfaces of cadmium sulfide quantum dots. Direct calorimetric measurements of the adsorption energies of such ligands have previously proven to be challenging because they are tightly adsorbed to the quantum dot surface. Here, we show that tetrahydrofuran can be used as a coordinating solvent, allowing cadmium oleates to more easily be …

The physiological acrosome reaction occurs after mammalian spermatozoa undergo a process called capacitation in the female reproductive tract. Only acrosome reacted spermatozoon can penetrate the egg zona-pellucida and fertilize the egg. Sperm also contain several mechanisms that protect it from undergoing spontaneous acrosome reaction (sAR), a process that can occur in sperm before reaching proximity to the egg and that abrogates fertilization. We previously showed that calmodulin-kinase II (CaMKII) and phospholipase D (PLD) are involved in preventing sAR through two distinct pathways that enhance F-actin formation during capacitation. Here, we describe a novel additional pathway involving the tyrosine kinase Fer in a mechanism that also prevents sAR by enhancing actin polymerization during sperm capacitation. We further show that protein-kinase A (PKA) and the tyrosine-kinase Src, as well as …

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 10 17 steps and thereby also study finite-time crossover phenomena.

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.

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.

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.

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 …

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 …