BINA

Analysis of an individual's immunoglobulin (IG) gene repertoire requires the use of high-quality germline gene Reference Sets. The Adaptive Immune Receptor Repertoire-Community (AIRR-C) Reference Sets have been developed to include only human IG heavy and light chain alleles that have been confirmed by evidence from multiple high-quality sources. By including only those alleles with a high level of support, including some new sequences that currently lack official names, AIRR-seq analysis will have greater accuracy and studies of the evolution of immunoglobulin genes, their allelic variants and the expressed immune repertoire will be facilitated. Although containing less than half the previously recognised IG alleles (e.g. just 198 IGHV sequences), the Reference Sets eliminated erroneous calls and provided excellent coverage when tested on a set of repertoires from 99 individuals comprising over 4 million V(D)J rearrangements. To improve AIRR-seq analysis, some alleles have been extended to deal with short 3' or 5' truncations that can lead them to be overlooked by alignment utilities. To avoid other challenges for analysis programs, exact paralogs (e.g. IGHV1-69*01 and IGHV1-69D*01) are only represented once in each set, though alternative sequence names are noted in accompanying metadata. The Reference Sets also include novel alleles: 8 IGHV alleles, 2 IGKV alleles and 5 IGLV alleles. The version-tracked AIRR-C Reference Sets are freely available at the OGRDB website (https://ogrdb.airr-community.org/germline_sets/Human) and will be regularly updated to include newly-observed and previously-reported …

The ban on many chemical pesticides has facilitated interest in discovery and application of bacteria (termed biocontrol agents) that antagonize soilborne plant pathogens. These bacteria protect plants from pathogens through a variety mechanisms that include niche exclusion (Wang et al., 2021), metabolic competition (Spadaro et al., 2010), production of siderophores (Yu et al., 2010; Li et al., 2014), secretion of chitinases that target the chitin components of fungal cell walls (Veliz et al., 2017), antibacterial and antifungal compounds (Raaijmakers et al., 2002; Ongena and Jacques, 2008), and induction of plant resistance (Pieterse et al., 2014). Secondary metabolites (SM),

Unconventional superconductivity was realized in systems comprising a monolayer of magnetic adatoms adsorbed on conventional superconductors, forming Shiba‐bands. Another approach to induce unconventional superconductivity and 2D Shiba‐bands was recently introduced, namely, by adsorbing chiral molecules (ChMs) on conventional superconductors, which act in a similar way to magnetic impurities as verified by conductance spectroscopy. However, the fundamental effect ChMs have on the strength of superconductivity has not yet been directly observed and mapped. In this work, local magnetic susceptometry is applied on heterostructures comprising islands of ChMs (α‐helix L‐polyalanine) monolayers adsorbed on Nb. It is found that the ChMs alter the superconducting landscape, resulting in spatially‐modulated weaker superconductivity. Surprisingly, the reduced diamagnetic response is located …

Metamaterials and plasmonic structures made from aluminum (Al) have attracted significant interest due to their low cost, long-term stability, and the relative abundance of aluminum compared to the rare metals. Also, aluminum displays distinct dielectric properties allowing for the excitation of surface plasmons in the ultraviolet region with minimal non-radiative losses. Despite these clear advantages, most of the research has been focused on either gold or silver, probably due to difficulties in forming smooth thin films of aluminum. In the present work, we detect and characterize second harmonic generation (SHG) in the optical regime, emanating from triangular hole arrays milled into thin aluminum films in reflection mode, at normal incidence. We report intense nonlinear responses, year-long stability, and overall superior performances with respect to gold. The robustness of the Al structures and high reproducibility …

Pelvic organ prolapse (POP) is a dysfunction that affects a large proportion of women. Current support scaffolds’ lack of biocompatibility, biodegradability, and mechanical compliance are associated with surgical complications including erosion and pain, indicating the urgent need for new tissue scaffolds with customizable functions. A new material that uses polyvinyl alcohol (PVA) as the main ingredient and is chemically tuned to possess suitable mechanical properties and degradation rates for the surgical treatment of POP is developed. Specifically, the thiol‐norbornene “click” chemistry enables the sol‐gel transition of the biomaterial under UV‐light without side‐products. Meanwhile, NaOH treatment further toughens the hydrogel with a higher crosslink density. The PVA‐based biocompatible ink can be printed with UV‐facilitated direct ink writing due to the rapidly UV‐initiated chemical crosslink; in situ image …

Although non-alkaline rechargeable Zn–air batteries (RZABs) are promising for energy storage, their chemistry is still underdeveloped and unclear. It was suggested that using Zn(OAc)2 or Zn(OTf)2 aqueous solutions as electrolytes enables reversible, corrosion-free charge–discharge processes, but the anodic stability of carbon in these cells has remained poorly studied. We report that CO2 evolution is manifested during the oxygen evolution reaction in non-alkaline RZABs, which is associated with the corrosion of carbon scaffolds. This corrosion is observed for different electrolyte compositions, such as Zn(OAc)2, ZnSO4 and Zn(OTf)2 solutions of various concentrations. The corrosion rate decreases when the overpotentials during the oxygen evolution reaction are lower. This study underlines the importance of addressing the anodic instability of carbon in non-alkaline RZABs.

Recovery from damage in materials helps extend their useful lifetime and of devices that contain them. Given that the photodamages in HaP materials and based devices are shown to recover, the question arises if this also applies to mechanical damages, especially those that can occur at the nanometer scale, relevant also in view of efforts to develop flexible HaP‐based devices. Here, this question is addressed by poking HaP single crystal surfaces with an atomic force microscope (AFM) tip under both ultra‐high vacuum (UHV) and variably controlled ambient water vapor pressure conditions. Sequential in situ AFM scanning allowed real‐time imaging of the morphological changes at the damaged sites. Using methylammonium (MA) and cesium (Cs) variants for A‐site cations in lead bromide perovskites, the experiments show that nanomechanical damages on methylammonium lead bromide (MAPbBr3) crystals …

TiO2 material has gained significant attention for large‐scale energy storage due to its abundant, low‐cost, and environmentally friendly properties, as well as the availability of various nanostructures. Phosphorus doping has been established as an effective technique for improving electronic conductivity and managing the slow ionic diffusion kinetics of TiO2. In this study, non‐doped and phosphorus doped TiO2 materials were synthesized using sodium alginate biopolymer as chelating agent. The prepared materials were evaluated as anode materials for Lithium‐Ion Batteries (LIBs). The electrodes exhibit remarkable electrochemical performance, including a high reversible capacity of 235 mAh g‐1 at 0.1C and excellent first coulombic efficiency of 99%. An integrated approach, combining Operando XRD and Ex‐situ XAS, comprehensively investigates the relationship between phosphorus doping, material …

Ultrasonic irradiation of molten metals in liquid media causes dispersion of the metals into suspensions of micro- and nanoparticles that can be separated. This is applicable mainly to low-mp elemental metals or alloys, but higher mp elemental metals or alloys were also reported. Among metals, mercury and gallium exhibit especially-low melting points and are thus considered as liquid metals (LMs). Sonication of mercury in aqueous solutions of certain metal ions can cause simultaneous reduction of the ions and reactions between the metals. Gallium can be melted and sonicated in warm water, as well as in aqueous solutions of various solutes such as metal ions and organic compounds, which opened a wide window of interactions between the gallium particles and the solutes. Sonication of molten metals in organic liquids, such as polyethylene glycol (PEG) 400, forms carbon dots (C-dots) doped with …

One of the problems associated with conducting a membrane filtration process is the accumulation of undesirable material on the surface of membranes. The deposited layer can significantly increase the resistance of the membrane, which leads to a reduction of the process efficacy. In many cases, the service life of the membranes is also reduced. One type of contamination that can accumulate on the surface of membranes are biological species (i.e., microorganisms). The process is called biofouling and can lead to a biofilm formation, which constitutes an integral layer resistant or completely invulnerable to many commonly used cleaning techniques. Various microorganisms, including bacteria, fungi and algae, proliferate and colonize the available surface of the membranes. Adhesion to the surface is enabled by secreted components known as extracellular polymeric substances, thanks to which a biofilm is formed on the surface. In order to reduce the intensity of biofouling, the membranes are subjected to various modification techniques. One of the modification techniques is the addition of particles with antimicrobial and anti-biofouling properties to the polymer at the stage of membrane production. In this study, copper oxide (CuO) was used as an antimicrobial material, which was added, as a nanopowder, to a polysulfone solution. From the prepared membrane-forming solution, flat ultrafiltration membranes were produced using the wet phase inversion method. The secondary solvent was the ultrapure water. The aim of the conducted research was to produce membranes with anti-biofouling properties and to characterize them in terms of …

Background Machine learning (ML) has gained significant attention for classifying immune states in adaptive immune receptor repertoires (AIRRs) to support the advancement of immunodiagnostics and therapeutics. Simulated data are crucial for the rigorous benchmarking of AIRR-ML methods. Existing approaches to generating synthetic benchmarking datasets result in the generation of naive repertoires missing the key feature of many shared receptor sequences (selected for common antigens) found in antigen-experienced repertoires. Results We demonstrate that a common approach to generating simulated AIRR benchmark datasets can introduce biases, which may be exploited for undesired shortcut learning by certain ML methods. To mitigate undesirable access to true signals in simulated AIRR datasets, we devised a simulation strategy (simAIRR) that constructs …

Nanoscale Page 1 Nanoscale rsc.li/nanoscale The Royal Society of Chemistry is the world's leading chemistry community. Through our high impact journals and publications we connect the world with the chemical sciences and invest the profits back into the chemistry community. IN THIS ISSUE ISSN 2040-3372 CODEN NANOHL 15(17) 7595–8030 (2023) Cover See Munho Kim, Guo-En Chang et al., pp. 7745–7754. Image reproduced by permission of Guo-En Chang from Nanoscale, 2023, 15, 7745. Inside cover See Palyam Subramanyam, Vasudevanpillai Biju et al., pp. 7695–7702. Image reproduced by permission of Vasudevanpillai Biju from Nanoscale, 2023, 15, 7695. REVIEWS 7608 Integration of functional peptides into nucleic acid-based nanostructures Jessica S. Freitag, Christin Möser, Robel Belay, Basma Altattan, Nico Grasse, Bhanu Kiran Pothineni, Jörg Schnauß and David M. Smith* 7625 …

The unique fluorescent nanomaterials known as carbon dots (CDs) are highly resistant to photobleaching, have low toxicity, and are well soluble in water. Polyethyleneimine (PEI) coated CDs are a novel fluorophore with good biocompatibility and pH sensing ability. Here, p-phenylenediamine (p-PD) is used as a carbon source and hyperbranched PEI is used as a surface passivation agent in a simple, one-step hydrothermal synthesis process. The CDs optical characteristics are pH-responsive due to the presence of different amine groups on PEI, which is functional polycationic polymer. The limits of techniques based on fluorescence intensity can be overcome by fluorescent lifetime imaging microscopy (FLIM), a very sensitive method for detecting a microenvironment. In this study, FLIM was used to measure pH with pH-sensitive CDs. These molecules are nontoxic to the cells, and the positively charged CDs have …

Morphogenesis involves the transformation of initially simple shapes, such as multicellular spheroids, into more complex 3D shapes. These shape changes are governed by mechanical forces including molecular motor-generated forces as well as hydrostatic fluid pressure, both of which are actively regulated in living matter through mechano-chemical feedback. Inspired by autonomous, biophysical shape change, such as occurring in the model organism hydra, we introduce a minimal, active, elastic model featuring a network of springs in a globe-like spherical shell geometry. In this model there is coupling between activity and the shape of the shell: if the local curvature of a filament represented by a spring falls below a critical value, its elastic constant is actively changed. This results in deformation of the springs that changes the shape of the shell. By combining excitation of springs and pressure regulation, we …

Micro- and Nano-particles are elemental for many current and developing technologies. Specifically, these particles are being extensively used in biological studies and applications, including imaging, drug delivery and therapeutics. Recent advances have led to the development of multifunctional particles, which have the potential to further enhance their effectiveness, enabling novel applications. Therefore, many efforts are devoted to produce well-defined particles for specific needs. However, conventional fabrication methodologies utilized to develop particles are time consuming, making it extremely challenging to fine-tune properties of the particles for multifunctional applications. Herein, we present a simple and facile method to fabricate dome-shaped micron and nano particles by a robust physical route. The presented method enables to design particles with a vast range of materials, sizes and compositions …

Micro- and nano-particles are elemental for many current and developing technologies. Specifically, these particles are being used extensively in biological studies and applications, which include imaging, drug delivery and therapeutics. Recent advances have led to the development of multifunctional particles, which have the potential to further enhance their effectiveness, enabling novel applications. Therefore, many efforts have been devoted to producing well-defined particles for specific needs. However, the conventional fabrication methodologies used to develop particles are time consuming, making it extremely challenging to fine-tune the properties of the particles for multifunctional applications. Herein, we present a simple and facile method to fabricate dome-shaped micron- and nano-sized particles via a robust physical route. The presented method enables particles to be designed using a vast range of …

Because of the abundance and availability of natural sea water resources, electrolysis of sea water is regarded as a most appealing and promising approach for the generation of hydrogen green energy, and even it lowers the cost of hydrogen production. However, for seawater electrolysis, highly efficient and robust electrocatalysts that can withstand chloride corrosion on electrodes, particularly the anode, are required. Here, we present the synthesis of nickel molybdenum phosphide engineered with ruthenium supported on nickel foam (Ru22NiMoP2/NF) by hydrothermal technique and followed reactions under autogenic pressure at elevated temperatures (RAPET) in Swagelok, which demonstrated excellent electrocatalytic activity in alkaline sea water. For hydrogen evolution reaction (HER), Ru22NiMoP2/NF requires low overpotentials of 60 and 52 mV to achieve a current density of 10 mAcm-2 than commercial …

Chiral polymeric particles (CPPs) were studied extensively in recent years due to their importance in pharmaceutical applications. Here, nanosized CPPs were synthesized and applied as catalysts for direct asymmetric aldol reaction. The CPPs were prepared by miniemulsion or inverse miniemulsion based on various chiral amino acid derivatives and characterized by dynamic light scattering and scanning electron microscopy. The nanoparticles with spherical structure between 250 and 400 nm and high chiral surface area were used as catalysts in the aldol reaction at room temperature without additional solvent. L-tryptophan gave the highest enantiomeric excess, >86% with similar catalytic performance four times.

Micelle Encapsulation Zinc‐doped copper oxide nanocomposites (MEnZn‐CuO NPs) is a novel doped metal nanomaterial prepared by our group based on Zinc doped copper oxide nanocomposites (Zn‐CuO NPs) using non‐micellar beam. Compared with Zn‐CuO NPs, MEnZn‐CuO NPs have uniform nanoproperties and high stability. In this study, we explored the anticancer effects of MEnZn‐CuO NPs on human ovarian cancer cells. In addition to affecting cell proliferation, migration, apoptosis and autophagy, MEnZn‐CuO NPs have a greater potential for clinical application by inducing HR repair defects in ovarian cancer cells in combination with poly (ADP‐ribose) polymerase inhibitors for lethal effects.

Cancer remains a leading cause of death globally (1). The conventional methods of treatment offered are radiation (2), chemotherapy (3), immunotherapy (4), surgery, and recently nanotechnology (nanomedicine and nano-processes)(5). Every cancer treatment can be defined and evaluated based on its efficiency, selectivity, side effects, and economic cost (6). However, combining predictive models and advanced machine learning methods with these cancer therapies may enhance their overall efficiency and selectivity, as well as the safety of the patient.Radiation Therapy (RT), also known as radiotherapy, is a non-surgical intervention frequently used in cancer treatment (2). This method is based on a high-level focused dose of radiation directed toward the tumor. This deposit of highenergy radiation kills cancer cells or decelerates their growth by damaging their DNA (2). Nevertheless, the challenges of RT include damage to tumor-proximate normal cells, the inability to radiate minor tumors out of scope of the imaging scans, patient movement, and low oxygen supply (7, 8). Therefore, many researchers are working on the development of targeted radiation methods to deliver a higher dose of radiation to the tumor with improved selectivity. Recently, the combination of nanotechnology with laser radiation has been demonstrated to represent a safe set of modalities for tumor destruction with high specificity (9). In particular, this involves the use of light-controlled nanoparticles (NPs) that can be activated via a light of a specific wavelength to form highly efficient and selective systems in the nanometer range (10). These NPs accumulate specifically …

Among numerous approaches for treating cancer, clinically approved photodynamic therapy (PDT) is considered a promising non‐invasive therapeutic strategy for solid tumors. While PDT has distinct advantages over conventional cancer treatments, systemic exposure to the photosensitizer and its stability are some of the limitations of clinical PDT. Herein, a therapeutic strategy for highly localized focal PDT is introduced based on direct biolistic delivery of photosensitizer‐loaded carriers to cancerous tumors. Degradable porous silicon microparticles (PSiMPs) are used as efficient carriers for the photosensitizer, meso‐tetrahydroxy‐phenylchlorin (mTHPC), and its conjugates with gold nanoparticles (AuNP‐mTHPC conjugates). The loaded PSiMP carriers are successfully bombarded using a pneumatic gene gun to breast cancer cells in vitro and into tumor xenografts in vivo, and subsequent uptake of the released …