BINA

The time-multiplexing super resolution concept requires post-processing for extracting the super-resolved image. Moreover, to perform the post-processing image restoration one needs to know the exact high-resolution encoding pattern. Both of these limiting conditions are overcome by the method and experiment reported in this Letter.

Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is a valuable experimental tool to study the immune state in health and following immune challenges such as infectious diseases, (auto)immune diseases, and cancer. Several tools have been developed to reconstruct B cell and T cell receptor sequences from AIRR-seq data and infer B and T cell clonal relationships. However, currently available tools offer limited parallelization across samples, scalability or portability to high-performance computing infrastructures. To address this need, we developed nf-core/airrflow, an end-to-end bulk and single-cell AIRR-seq processing workflow which integrates the Immcantation Framework following BCR and TCR sequencing data analysis best practices. The Immcantation Framework is a comprehensive toolset, which allows the processing of bulk and single-cell AIRR-seq data from raw read processing to clonal inference. nf-core/airrflow is written in Nextflow and is part of the nf-core project, which collects community contributed and curated Nextflow workflows for a wide variety of analysis tasks. We assessed the performance of nf-core/airrflow on simulated sequencing data and show example results with real datasets. To demonstrate the applicability of nf-core/airrflow to the high-throughput processing of large AIRR-seq datasets, we validated and extended previously reported findings of convergent antibody responses to SARS-CoV-2 by analyzing 97 COVID-19 infected individuals and 99 healthy controls retrieved from public databases. nf-core/airrflow is available free of charge, under the MIT license on GitHub (https://github.com/nf-core …

Tissue Optics and Photonics III Page 1 PROCEEDINGS OF SPIE Volume 13010 Proceedings of SPIE 0277-786X, V. 13010 SPIE is an international society advancing an interdisciplinary approach to the science and application of light. Tissue Optics and Photonics III Valery V. Tuchin Walter C. Blondel Zeev Zalevsky Editors 9–11 April 2024 Strasbourg, France Sponsored by SPIE Cooperating Organisations Photonics 21 (Germany) EOS—European Optical Society (Germany) Published by SPIE Tissue Optics and Photonics III, edited by Valery V. Tuchin, Walter CPM Blondel, Zeev Zalevsky, Proc. of SPIE Vol. 13010, 1301001 · © 2024 SPIE 0277-786X · doi: 10.1117/12.3037614 Proc. of SPIE Vol. 13010 1301001-1 Page 2 The papers in this volume were part of the technical conference cited on the cover and title page. Papers were selected and subject to review by the editors and conference program committee. Some …

Calcium (Ca) metal batteries, due to the high crustal abundance and potential for dendrite-free cycling of Ca, are promising alternative to current lithium battery chemistry. Ca deposition in aprotic organic electrolytes had been stalled by ion-blocking passivation layers on Ca metal. This limitation was recently overcome by using borate-based electrolyte solutions, but the electrode/electrolyte interfacial chemistry enabling reversible Ca metal deposition remains unclear. This study elucidates the formation and dynamic evolution of passivation layers upon immersion of Ca metal electrodes and during electrochemical Ca deposition/dissolution processes in a representative calcium tetrakis(hexafluoroisopropyloxy)-borate (Ca[B(hfip)4]2) and glyme electrolyte solution. Upon ageing, a native passivation layer comprising porous Ca metal and Ca ion conducting solid-electrolyte interphase is formed. In subsequent …

This study delves into the critical role of customized material design and synthesis methods in influencing the performance of electrocatalysts for oxygen reduction reaction (ORR) in anion exchange membrane fuel cells (AEMFCs). It introduces a novel approach to obtain platinum-free electrocatalysts (PGM-free), based on the controlled integration of iron active sites onto the surface of silica nanoparticles (NPs) by using nitrogen-based surface ligands. These NPs are used as hard templates to form tailored nanostructured electrocatalysts with an improved iron dispersion into the carbon matrix. Utilizing a wide array of analytical techniques including infrared and X-ray photoelectron spectroscopies, X-ray diffraction and surface area measurements, this work provides insight into the physical parameters that are critical for the ORR electrocatalysis with PGM-free electrocatalysts. These findings underscore the potential …

Photo‐induced evolution of statistically rough surfaces of amorphous chalcogenide films As20Se80 at room temperature has been studied by measuring the angular dependence of the intensity of light scattered from a surface illuminated by cw laser (λ = 660 nm). The interpretation of the scattering data based on the resonant scattering theory enabled to confirm unequivocally the diffusion mechanism of PI mass transfer. It was detected that the change of the amplitude of a spatial harmonic in the roughness spectra strongly depended on its period Λ. During illumination, the amplitude increased at Λ > Λ∗, whereas harmonics with Λ < Λ∗ decreased. Λ∗ , which corresponds to zero evolution rate. was found to be 6.7 μm. In accordance with our theoretical prediction, both growth and decrease were exponential with the rates depended on Λ. As the result, the roughness with initial rms height of 50 ‐ 70 nm transformed …

Photon‐number‐splitting (PNS) is a well‐known theoretical attack on quantum key distribution (QKD) protocols that employ weak coherent states produced by attenuated laser pulses. However, beyond the fact that it has not yet been demonstrated experimentally, its plausibility and effect on quantum bit error rate are questioned. In this work, an experimental scheme is presented for PNS attack employing demonstrated technological capabilities, specifically a single‐photon Raman interaction (SPRINT) in a cavity‐enhanced three‐level atomic system. Several aspects of the proposed implementation are addressed, analytically and simulatively, and the eavesdropper's information gain by the attack is calculated. Furthermore, it is analytically shown that the scheme results in a small (yet non‐zero) quantum bit error rate, and a comparison to purely theoretical analyses in the literature is presented. It is believed that the …

Pharmaceutical waste and contaminants pose a significant global concern for water and food safety. The detection of piperidine, a common residue in drug and supplement synthesis, is critical due to its toxic nature to both humans and animals. In this study, we develop a plasmonic-based detector for surface enhanced Raman scattering (SERS) measurements. The plasmonic device is composed of triangular cavities, milled in silver thin film, and protected by a 5 nm SiO2 layer. Due to the confined and enhanced electromagnetic field, remarkable sensitivity to piperidine with a concentration of 10−8 M in water is achieved. Despite the relatively small polarizability of piperidine, high sensitivity is observed even when using a low numerical aperture of 0.3, attributed to the directional scattering from our plasmonic device. Thus, it offers a cost-effective alternative to traditional high numerical aperture used in SERS, and the …

Magnesium batteries have attracted considerable attention as a promising technology for future energy storage because of their capability to undergo multiple charging reactions. However, most oxide materials utilized as hosts for magnesium batteries do not perform well at room temperature or in nonaqueous electrolytes. Herein, a host material, Na0.04MoO3·(H2O)0.49 is successfully developed through the chemical reduction of alpha‐MoO3, which enables magnesium storage reaction in a 0.5 m Mg(ClO4)2/acetonitrile electrolyte at 25 °C. Electrochemical analysis reveals that the cathode material possesses a discharge capacity of 157.4 mAh g−1 at a 0.2 C rate. The Na0.04MoO3·(H2O)0.49 cathode material also exhibits a capacity retention of 93.4% after 100 cycles compared to the first cycle at a 2 C rate, with an average discharge voltage of −0.474 V versus activated carbon (≈2.16 V estimated …

Topological insulators, a class of materials possessing bulk bandgap and metallic surface states with a topological nontrivial symmetry, are considered promising candidates for emerging quantum and optoelectronic applications. However, achieving scalable growth and control over parameters including thickness, carrier density, bulk bandgap, and defect density remains a challenge in realizing such applications. In this work, we show the scalable growth of topological insulator alloys Bi2Se(3-x)Sx and demonstrate composition-tunable bandgap, using chemical vapor deposition (CVD). A bandgap increase of up to ~40% at a sulfur concentration of ~15% is demonstrated. Correspondingly, the real part (n) of the refractive index is reduced in the alloy by ~25% relative to that of Bi2Se3. Additionally, electronic transport measurements indicate a bulk p-type doping and field-effect tunable metallic surface states of the …

The maintenance of a properly folded proteome is critical for cellular function and organismal health, and its age-dependent collapse is associated with a wide range of diseases. Here, we find that despite the central role of Coenzyme A as a molecular cofactor in hundreds of cellular reactions, limiting Coenzyme A levels in C. elegans and in human cells, by inhibiting the conserved pantothenate kinase, promotes proteostasis. Impairment of the cytosolic iron-sulfur clusters formation pathway, which depends on Coenzyme A, similarly promotes proteostasis and acts in the same pathway. Proteostasis improvement by Coenzyme A/iron-sulfur cluster deficiencies are dependent on the conserved HLH-30/TFEB transcription factor. Strikingly, under these conditions, HLH-30 promotes proteostasis by potentiating the expression of select chaperone genes providing a chaperone-mediated proteostasis shield, rather than by its established role as an autophagy and lysosome biogenesis promoting factor. This reflects the versatile nature of this conserved transcription factor, that can transcriptionally activate a wide range of protein quality control mechanisms, including chaperones and stress response genes alongside autophagy and lysosome biogenesis genes. These results highlight TFEB as a key proteostasis-promoting transcription factor and underscore it and its upstream regulators as potential therapeutic targets in proteostasis-related diseases

Membrane potential (MP) changes can provide a simple readout of bacterial functional and metabolic state or stress levels. While several optical methods exist for measuring fast changes in MP in excitable cells, there is a dearth of such methods for absolute and precise measurements of steady-state membrane potentials (MPs) in bacterial cells. Conventional electrode-based methods for the measurement of MP are not suitable for calibrating optical methods in small bacterial cells. While optical measurement based on Nernstian indicators have been successfully used, they do not provide absolute or precise quantification of MP or its changes. We present a novel, calibrated MP recording approach to address this gap. Our method is based on (i) a unique VoltageFluor (VF) optical transducer, whose fluorescence lifetime varies as a function of MP via photoinduced electron transfer (PeT) and (ii) a quantitative phasor-FLIM analysis for high-throughput readout. This method allows MP changes to be easily recorded, quantified and visualized. Using our preliminary Bacillus subtilis-specific MP versus VF lifetime calibration, we estimated the MP for unperturbed B. subtilis cells to be -65 mV and that for chemically depolarized cells as -14 mV. Our work paves the way for deeper insights into bacterial electrophysiology and bioelectricity research.

Accumulated evidence of transgenerational inheritance of epigenetic and symbiotic changes begs the question of whether (and under which conditions) the population can benefit from inheritance of changes that are acquired during the individuals' lifetime. To address this question, we introduce a population epigenetics model of individuals undergoing stochastic and/or induced changes that are either partially or fully transmitted to the offspring. This model is equally applicable to internal changes in individuals (e.g. epigenetic and symbiotic variations) as well as niche construction changes that they make in their environment. Potentially adaptive and maladaptive responses are represented, respectively, by induced changes that reduce and increase the individuals' rate of death (i.e. reduction and increase of selective pressure). We use this framework to investigate how inheritance of acquired changes affects the long-term dynamics of the population. Analytic solution in a simple case of a population exposed to environments that change in time shows that inheritance of changes that transiently alleviate the selective pressure is beneficial even when the offspring environment differs from that of their parents. The benefit from these changes is even more pronounced at lower fidelity of inheritance as well as for populations with age-dependent decline in fertility. We also show that this benefit is essential for preventing population extinction under a range of successive shifts in the environment. Analysis of long-term influences of various population and environmental factors reveals a non-trivial landscape of outcomes, including a surprising regime in …

Lead chalcogenides are compelling materials for nanophotonics and optoelectronics due to their high refractive indices, extreme thermo‐optic coefficients, and high transparency in the mid‐infrared (MIR). In this study, PbTe hoppercubes (HC, face‐open box cubes) are synthesized and explored for their MIR resonant characteristics. Single‐particle microspectroscopy uncovered deep‐subwavelength light localization, with a spectral response dominated by both fundamental and multiple high‐order Mie‐resonant modes. Nanoimaging mapping using scattering‐type scanning near‐field optical microscopy (s‐SNOM) reveals that the scattering at the center of the HC is reduced by more than five times compared to the edges. 2D‐Hyperspectral scans conducted using a low‐power broadband MIR source and nanometer spatial resolutions provided information on the local amplitude and phase‐resolved near‐fields …

Complete decarbonization of hard-to-abate industrial sectors is critical to reach the carbon neutrality goal set for 2050. The production of nitrogen-containing fertilizers (N-fertilizers) is responsible for 2.1% of the overall global carbon dioxide emissions. Urea is the most common N-fertilizer, and it is currently produced through the Bosch-Meiser process starting from ammonia (NH3) and carbon dioxide (CO2). Electrochemical production of urea can reduce drastically the emission of greenhouse gases and the energy required for the process. Promising results were recently reported using nitrate (NO3-) and CO2 as reagents with increasing production rate and Faradaic efficiency. In this mini-review, we summarize the most recent studies, including reaction mechanisms, electrocatalysts, and detection methods, highlighting the challenges in the field. A roadmap for future developments is envisioned with the scope of …

Verena A. Neufeld opened a general discussion of the paper by Andreas Grüneis: In Table 6 of your article (https://doi. org/10.1039/d4fd00085d), EX top-fcc with CCSD (cT) is 0.41 eV which is similar in magnitude to the (cT)-corr. contribution (− 0.44 eV). How con dent can we be about the EX top and EX fcc comparison at the CCSD (cT) level since full con guration interaction could lower EX top-fcc further?Andreas Grüneis responded: Thank you for raising this important point. On the one hand, we agree that the large triples contribution indicate that higherorder correlation effects could be important. If possible, one should try to apply FCIQMC or other cost-effective and accurate approaches to this system and provide benchmark numbers for CC. On the other hand, the reasonable agreement with the experimentally measured adsorption energy suggests, that higherorder effects could potentially cancel out or are …

This study delves into the critical role of customized materials design and synthesis methods in influencing the performance of electrocatalysts for the oxygen reduction reaction (ORR) in anion exchange membrane fuel cells (AEMFCs). It introduces a novel approach to obtain platinum-free (PGM-free) electrocatalysts based on the controlled integration of iron active sites onto the surface of silica nanoparticles (NPs) by using nitrogen-based surface ligands. These NPs are used as hard templates to form tailored nanostructured electrocatalysts with an improved iron dispersion into the carbon matrix. By utilizing a wide array of analytical techniques including infrared and X-ray photoelectron spectroscopy techniques, X-ray diffraction and surface area measurements, this work provides insight into the physical parameters that are critical for ORR electrocatalysis with PGM-free electrocatalysts. The new catalysts showed a …

The time-multiplexing super resolution concept requires post-processing for extracting the super-resolved image. Moreover, to perform the post-processing image restoration one needs to know the exact high-resolution encoding pattern. Both of these limiting conditions are overcome by the method and experiment reported in this Letter.

Currently, layered Ni-rich oxides cathodes of LiNi1-xMnyCozO2 (x ≥ 0.8) have gained a major attention for the high energy density Li-ion batteries (LIBs), due to their high specific capacity of ~200 mAh g-1 within the limited voltage. However, the large-scale use of these cathodes is severely limited by the poor structural stability, high surface reactivity, and severe capacity fade resulting from the intergranular micro cracks triggered by large volume changes and formation of rock salts at highly de-lithiated state. Knowing the demand for high specific capacity and high cycling stability, a core-shell oxide material 0.8LiNi0.85Mn0.10Co0.05O2-0.2Li1.2Ni0.16Mn0.56Co0.08O2 (NR-CS) with a core Ni-rich oxide, LiNi0.85Mn0.10Co0.05O2 (NMC85) and an outer shell of Mn-based Li-rich Li1.2Ni0.16Mn0.56Co0.08O2 oxide is synthesized, which delivers an initial discharge capacity of 212 mAh g-1 when cycled at 20 mA g -1 …

Approximately 10% of Renal Cell Carcinoma (RCC) tumors form a thrombus that invades into nearby vasculature and is associated with lower survivability. However, the mechanisms driving tumor thrombus formation and progression are poorly understood. We therefore examined a publicly available RNAseq dataset of samples from RCC patients containing tumors with and without thrombi, as well as associated normal kidney tissues, and compared them. Using cell deconvolution, we found indications that kidney tumors and thrombi are associated with loss of mature kidney-specific cell types and gain of proliferative characteristics. Moreover, we identified a set of transcripts that are alternatively spliced between tumors with and without thrombi. Using motif enrichment analysis for known RNA binding proteins we found putative splicing regulators that are presumably associated with thrombus formation. We believe that this study will assist in unraveling cellular and molecular mechanisms of tumor progression and thrombus formation in RCC.

The innate immune sensor PKR for double-stranded RNA (dsRNA) is critical for antiviral defense, but its aberrant activation by cellular dsRNA is linked to various diseases. The dsRNA-binding protein PACT plays a critical yet controversial role in the PKR pathway. We demonstrate that PACT is a direct and specific suppressor of PKR against endogenous dsRNA ligands like inverted-repeat Alu RNAs, which robustly activate PKR in the absence of PACT. PACT-mediated inhibition does not involve competition for dsRNA binding. Instead, PACT impairs PKR ability to scan along dsRNA, a process necessary for PKR molecules to encounter and autophoshorylate each other for activation. By scanning along dsRNA and directly interacting with PKR, PACT restricts PKR movement on dsRNA, reducing the likelihood of PKR molecular collisions and subsequent autophosphorylation, effectively inhibiting PKR without sequestering dsRNA. Consequently, PKR inhibition is more robust with longer and less abundant dsRNA, and minimal with abundant or short dsRNA. Thus, PACT functions to adjust the PKR activation threshold for long endogenous dsRNA without altering its inherent activity, revealing new mechanisms for establishing self-tolerance.