BINA

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.

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 …

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.

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.

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.

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.

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 …

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 …

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 …

Superconducting flux qubits are promising candidates for the physical realization of a scalable quantum processor. Indeed, these circuits may have both a small decoherence rate and a large anharmonicity. These properties enable the application of fast quantum gates with high fidelity and reduce scaling limitations due to frequency crowding. The major difficulty of flux qubits' design consists of controlling precisely their transition energy - the so-called qubit gap - while keeping long and reproducible relaxation times. Solving this problem is challenging and requires extremely good control of e-beam lithography, oxidation parameters of the junctions and sample surface. Here we present measurements of a large batch of flux qubits and demonstrate a high level of reproducibility and control of qubit gaps, relaxation times and pure echo dephasing times. These results open the way for potential applications in the fields of quantum hybrid circuits and quantum computation.

Stress granules (SGs) can assemble in cancer cells upon chemotoxic stress. Glucocorticoids function during stress responses and are administered with chemotherapies. The roles of glucocorticoids in SG assembly and disassembly pathways are unknown. We examined whether combining glucocorticoids such as cortisone with chemotherapies from the vinca alkaloid family, which dismantle the microtubule network, affects SG assembly and disassembly pathways and influences cell viability in cancer cells and human-derived organoids. Cortisone augmented SG formation when combined with vinorelbine (VRB). Live-cell imaging showed that cortisone increased SG assembly rates but reduced SG clearance rates after stress, by increasing protein residence times within the SGs. Mechanistically, VRB and cortisone signaled through the integrated stress response mediated by eIF2α (also known as EIF2S1 …

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 …

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 …

Doped Mott insulators exhibit some of the most intriguing quantum phases of matter, including quantum spin liquids, unconventional superconductors and non-Fermi liquid metals–. Such phases often arise when itinerant electrons are close to a Mott insulating state, and thus experience strong spatial correlations. Proximity between different layers of van der Waals heterostructures naturally realizes a platform for experimentally studying the relationship between localized, correlated electrons and itinerant electrons. Here we explore this relationship by studying the magnetic landscape of tantalum disulfide 4Hb-TaS2, which realizes an alternating stacking of a candidate spin liquid and a superconductor. We report on a spontaneous vortex phase whose vortex density can be trained in the normal state. We show that time-reversal symmetry is broken in the normal state, indicating the presence of a magnetic phase …

The two-dimensional electron system found between LaAlO3 and SrTiO3 hosts a variety of physical phenomena that can be tuned through external stimuli. This allows for electronic devices controlling magnetism, spin–orbit coupling, and superconductivity. Controlling the electron density by varying donor concentrations and using electrostatic gating are convenient handles to modify the electronic properties, but the impact on the microscopic scale, particularly of the former, remains underexplored. Here, we image the current distribution at 4.2 K in amorphous-LaAlO3/SrTiO3 using scanning superconducting quantum interference device microscopy while changing the carrier density in situ using electrostatic gating and oxygen annealing. We show how potential disorder affects the current and how homogeneous 2D flow evolves into several parallel conducting channels when approaching the metal-to-insulator …

In this work, we study a series of tunable flux qubits inductively coupled to a coplanar waveguide resonator fabricated on a sapphire substrate. Each qubit includes an asymmetric superconducting quantum interference device, which is controlled by the application of an external magnetic field and acts as a tunable Josephson junction. The tunability of the qubits is typically±3.5 GHz around their central gap frequency. The measured relaxation times are limited by dielectric losses in the substrate and can attain T 1∼ 8 μ s. The echo dephasing times are limited by flux noise even at optimal points and reach T 2 E∼ 4 μ s, almost an order of magnitude longer than state of the art.