bluuebunny/crossref_metadata_2025 huggingface dataset:
A protein vaccine of RBD integrated with immune evasion mutation shows broad protection against SARS-CoV-2
Authors: An Ran , Yang Hao , Tang Cong , Li Qianqian , Huang Qing , Wang Haixuan , Wang Junbin , Zhou Yanan , Yang Yun , Chen Hongyu , Yu Wenhai , Li Bai , Wu Daoju , Zhang Yong , Luo Fangyu , Quan Wenqi , Xu Jingwen , Lin Dongdong , Liang Xiaoming , Yan Yuhuan , Yuan Longhai , Du Xuena , Yuan Yuxia , Li Yanwen , Sun Qiangming , Wang Youchun , Lu Shuaiyao
Published: November 2024

Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to emerge and evade immunity, resulting in breakthrough infections in vaccinated populations. There is an urgent need for the development of vaccines with broad protective effects. In this study, we selected hotspot mutations in the receptor-binding domain (RBD) that contribute to immune escape properties and integrated them into the original RBD protein to obtain a complex RBD protein (cRBD), and we found cRBDs have broad protective effects against SARS-CoV-2 variants. Three cRBDs were designed in our study. Compared with the BA.1 RBD protein, the cRBDs induced the production of higher levels of broader-spectrum neutralizing antibodies, suggesting stronger and broader protective efficacy. In viral challenge experiments, cRBDs were more effective than BA.1 RBD in attenuating lung pathologic injury. Among the three constructs, cRBD3 showed optimal broad-spectrum and protective effects and is a promising candidate for a broad-spectrum SARS-CoV-2 vaccine. In conclusion, immunization with cRBDs triggered immunity against a wide range of variants, including those that emerged after we had completed designing the cRBDs. This study preliminarily explores and validates the feasibility of incorporating hotspot mutations that contribute to immune evasion into the RBD to expand the activity spectrum of antigen-induced antibodies.
Dependence of NPPS creates a targetable vulnerability in RAS-mutant cancers
Authors: Xia Rui-xue , Zou Pei-chen , Xie Jun-ting , Tang Ya-bin , Gong Miao-miao , Fan Fu , Aihemaiti Ayinazhaer , Liu Yu-qing , Shen Ying , Zhou Bin-bing S. , Zhu Liang , Lei Hui-min
Published: November 2024

RAS is the most frequently mutated oncoprotein for cancer driving. Understanding of RAS biology and discovery of druggable lynchpins in RAS pathway is a prerequisite for targeted therapy of RAS-mutant cancers. The recent identification of KRASG12C inhibitor breaks the “undruggable” curse on RAS and has changed the therapy paradigm of KRAS-mutant cancers. However, KRAS mutations, let alone KRASG12C mutation, account for only part of RAS-mutated cancers. Targeted therapies for cancers harboring other RAS mutations remain the urgent need. In this study we explored the pivotal regulatory molecules that allow for broad inhibition of RAS mutants. By comparing the expression levels of nucleotide pyrophosphatase (NPPS) in a panel of cell lines and the functional consequence of increased NPPS expression in RAS-mutant cells, we demonstrated that cancer cells with various kinds of RAS mutations depended on NPPS for growth and survival, and that this dependence conferred a vulnerability of RAS-mutant cancer to treatment of NPPS inhibition. RAS-mutant cells, compared with RAS-wildtype cells, bored and required an upregulation of NPPS. Transcriptomics and metabolomics analyses revealed a NPPS-dependent hyperglycolysis in RAS-mutant cells. We demonstrated that NPPS promoted glucose-derived glycolytic intermediates in RAS-mutant cells by enhancing its interaction with hexokinase 1 (HK1), the enzyme catalyzing the first committed step of glycolysis. Pharmacological inhibition of NPPS-HK1 axis using NPPS inhibitor Enpp-1-IN-1 or HK1 inhibitor 2-deoxyglucose (2-DG), or genetic interfere with NPPS suppressed RAS-mutant cancers in vitro and in vivo. In conclusion, this study reveals an unrecognized mechanism and druggable lynchpin for modulation of pan-mutant-RAS pathway, proposing a new potential therapeutic approach for treating RAS-mutant cancers.
Smad transcription factors as mediators of 7 transmembrane G protein-coupled receptor signalling
Authors: Chia Zheng-Jie , Kumarapperuma Hirushi , Zhang Ruizhi , Little Peter J. , Kamato Danielle
Published: November 2024

The Smad transcription factors are well known for their role at the core of transforming growth factor-β (TGF-β) signalling. However, recent evidence shows that the Smad transcription factors play a vital role downstream of other classes of receptors including G protein-coupled receptors (GPCR). The versatility of Smad transcription factors originated from the two regions that can be differently activated by the TGF-β receptor superfamily or through the recruitment of intracellular kinases stimulated by other receptors classes such as GPCRs. The classic GPCR signalling cascade is further expanded to conditional adoption of the Smad transcription factor under the stimulation of Akt, demonstrating the unique involvement of the Smad transcription factor in GPCR signalling pathways in disease environments. In this review, we provide a summary of the signalling pathways of the Smad transcription factors as an important downstream mediator of GPCRs, presenting exciting opportunities for discovering new therapeutic targets for diseases.
Mosaic chromosomal alterations (mCAs) in individuals with monoclonal B-cell lymphocytosis (MBL)
Authors: Sekar Aswin , Griffin Rosalie , Parikh Sameer A. , Genovese Giulio , Robinson Dennis P. , Norman Aaron D. , Olson Janet E. , Rabe Kari G. , Hoel Mingma S. , Boddicker Nicholas J. , Hampel Paul J. , Kay Neil E. , Cerhan James R. , Braggio Esteban , Hanson Curtis A. , Vachon Celine M. , Shanafelt Tait D. , Ebert Benjamin L. , Slager Susan L.
Published: November 2024

MBL is a precursor condition to chronic lymphocytic leukemia (CLL), characterized by monoclonal B-cells in blood. Mosaic chromosomal alterations (mCAs) are a form of clonal hematopoiesis that include gains, losses, and copy-neutral loss-of-heterozygosity of large DNA segments. Both MBL and mCAs have been found to increase the risk of CLL and lymphoid malignancies, and the aim of our study was to investigate how mCAs relate to MBL, which is currently unknown. We analyzed genetic, flow cytometric, and hematologic data from 4632 individuals from the Mayo Clinic Biobank and CLL Database. MBL was detected using flow cytometry and classified as high-count (HC) or low-count (LC) MBL based on clone size. mCAs were detected primarily from whole blood DNA using sensitive SNP-array-based analyses. mCAs commonly altered in CLL (deletion of 6q, 11q, 13q, 17p, and trisomy 12) were specific (>99%) to individuals with MBL and CLL. HC-MBL and LC-MBL individuals were 881-fold and 8-fold, respectively, more likely to harbor CLL-associated mCAs than those without MBL. The cell fraction bearing these mCAs typically exceeded the B-cell fraction, suggesting their origin prior to the B-cell lineage. Integrating genetic and blood count data enabled detecting HC-MBL with high specificity in a biobank sample. These results quantify the contribution of mCAs to MBL and could enable large studies of HC-MBL without the need for flow cytometric screening.
Measurable residual mutated IDH1 before allogeneic transplant for acute myeloid leukemia
Authors: Gui Gege , Ravindra Niveditha , Hegde Pranay S. , Andrew Georgia , Mukherjee Devdeep , Wong Zoë , Auletta Jeffery J. , El Chaer Firas , Chen Evan C. , Chen Yi-Bin , Corner Adam , Devine Steven M. , Iyer Sunil G. , Jimenez Jimenez Antonio Martin , De Lima Marcos J. G. , Litzow Mark R. , Kebriaei Partow , Saber Wael , Spellman Stephen R. , Zeger Scott L. , Page Kristin M. , Dillon Laura W. , Hourigan Christopher S.
Published: November 2024

Measurable residual disease (MRD) in adults with acute myeloid leukemia (AML) in complete remission is an important prognostic marker, but detection methodology requires optimization. Persistence of mutated NPM1 or FLT3-ITD in the blood of adult patients with AML in first complete remission (CR1) prior to allogeneic hematopoietic cell transplant (alloHCT) associates with increased relapse and death after transplant. The prognostic implications of persistence of other common AML-associated mutations, such as IDH1, at this treatment landmark however remain incompletely defined. We performed testing for residual IDH1 variants (IDH1m) in pre-transplant CR1 blood of 148 adult patients undergoing alloHCT for IDH1-mutated AML at a CIBMTR reporting site between 2013 and 2019. No statistically significant post-transplant differences were observed between those testing IDH1m positive (n = 53, 36%) and negative pre-transplant (overall survival (OS): p = 0.4; relapse: p = 0.5). For patients with IDH1 mutated AML co-mutated with NPM1 and/or FLT3-ITD, only detection of persistent mutated NPM1 and/or FLT3-ITD was associated with significantly higher rates of relapse (p = 0.01). These data, from the largest study to date, do not support the detection of IDH1 mutation in CR1 blood prior to alloHCT as evidence of AML MRD for increased post-transplant relapse risk.
Replication stress induces POLQ-mediated structural variant formation throughout common fragile sites after entry into mitosis
Authors: Wilson Thomas E. , Ahmed Samreen , Winningham Amanda , Glover Thomas W.
Published: November 2024

Genomic structural variants (SVs) greatly impact human health, but much is unknown about the mechanisms that generate the largest class of nonrecurrent alterations. Common fragile sites (CFSs) are unstable loci that provide a model for SV formation, especially large deletions, under replication stress. We study SV junction formation as it occurs in human cell lines by applying error-minimized capture sequencing to CFS DNA harvested after low-dose aphidicolin treatment. SV junctions form throughout CFS genes at a 5-fold higher rate after cells pass from G2 into M-phase. Neither SV formation nor CFS expression depend on mitotic DNA synthesis (MiDAS), an error-prone form of replication active at CFSs. Instead, analysis of tens of thousands of de novo SV junctions combined with DNA repair pathway inhibition reveal a primary role for DNA polymerase theta (POLQ)-mediated end-joining (TMEJ). We propose an important role for mitotic TMEJ in nonrecurrent SV formation genome wide.
Microscale chemical imaging to characterize and quantify corrosion processes at the metal-electrolyte interface
Authors: Albert Cristhiana C. , Mundra Shishir , Ferreira Sanchez Dario , Furcas Fabio E. , Rajyaguru Ashish D. , Isgor O. Burkan , Grolimund Daniel , Angst Ueli M.
Published: November 2024

We introduce an experimental setup to chemically image corrosion processes at metal-electrolyte interfaces under stagnant, confined conditions—relevant in a wide range of situations. The setup is based on a glass capillary, in which precipitation of corrosion products in the interfacial aqueous phase can be monitored over time with optical microscopy, and chemically and structurally characterized with microscopic synchrotron-based techniques (X-ray fluorescence, X-ray diffraction, and X-ray absorption spectroscopy). Moreover, quantification of precipitates through X-ray transmission measurements provides in-situ corrosion rates. We illustrate this setup for iron corrosion in a pH 8 electrolyte, revealing the critical role of O2 and iron diffusion in governing the precipitation of ferrihydrite and its transformation to goethite. Corrosion and coupled reactive transport processes can thus be monitored and fundamentally investigated at the metal-electrolyte interface, with micrometer-scale resolution. This capillary setup has potential applications for in-situ corrosion studies of various metals and environments.
Classification of dynamical Lie algebras of 2-local spin systems on linear, circular and fully connected topologies
Authors: Wiersema Roeland , Kökcü Efekan , Kemper Alexander F. , Bakalov Bojko N.
Published: November 2024

Much is understood about 1-dimensional spin chains in terms of entanglement properties, physical phases, and integrability. However, the Lie algebraic properties of the Hamiltonians describing these systems remain largely unexplored. In this work, we provide a classification of all Lie algebras generated by the terms of 2-local spin chain Hamiltonians, or so-called dynamical Lie algebras, on 1-dimensional linear and circular lattice structures. We find 17 unique dynamical Lie algebras. Our classification includes some well-known models such as the transverse-field Ising model and the Heisenberg chain, and we also find more exotic classes of Hamiltonians that appear new. In addition to the closed and open spin chains, we consider systems with a fully connected topology, which may be relevant for quantum machine learning approaches. We discuss the practical implications of our work in the context of variational quantum computing, quantum control and the spin chain literature.
Offline ensemble co-reactivation links memories across days
Authors: Zaki Yosif , Pennington Zachary T. , Morales-Rodriguez Denisse , Bacon Madeline E. , Ko BumJin , Francisco Taylor R. , LaBanca Alexa R. , Sompolpong Patlapa , Dong Zhe , Lamsifer Sophia , Chen Hung-Tu , Carrillo Segura Simón , Christenson Wick Zoé , Silva Alcino J. , Rajan Kanaka , van der Meer Matthijs , Fenton André , Shuman Tristan , Cai Denise J.
Published: November 2024

Memories are encoded in neural ensembles during learning1–6 and are stabilized by post-learning reactivation7–17. Integrating recent experiences into existing memories ensures that memories contain the most recently available information, but how the brain accomplishes this critical process remains unclear. Here we show that in mice, a strong aversive experience drives offline ensemble reactivation of not only the recent aversive memory but also a neutral memory formed 2 days before, linking fear of the recent aversive memory to the previous neutral memory. Fear specifically links retrospectively, but not prospectively, to neutral memories across days. Consistent with previous studies, we find that the recent aversive memory ensemble is reactivated during the offline period after learning. However, a strong aversive experience also increases co-reactivation of the aversive and neutral memory ensembles during the offline period. Ensemble co-reactivation occurs more during wake than during sleep. Finally, the expression of fear in the neutral context is associated with reactivation of the shared ensemble between the aversive and neutral memories. Collectively, these results demonstrate that offline ensemble co-reactivation is a neural mechanism by which memories are integrated across days.
Combined effect of nitrogen-doped carbon and NiCo2O4 for electrochemical water splitting
Authors: Kubińska Laura , Szkoda Mariusz , Skorupska Malgorzata , Grabowska Patrycja , Gajewska Marta , Lukaszewicz Jerzy P. , Ilnicka Anna
Published: November 2024

Electrocatalytic water splitting for green hydrogen production necessitates effective electrocatalysts. Currently, commercial catalysts are primarily platinum-based. Therefore, finding catalysts with comparable catalytic activity but lower cost is essential. This paper describes spinel-structured catalysts containing nickel cobaltite NiCo2O4, graphene, and additionally doped with heteroatoms. The structure and elemental composition of the obtained materials were analyzed by research methods such as TEM, SEM-EDX, XRD, XPS, and Raman spectroscopy. The electrochemical measurements showed that hybrid materials containing nickel cobaltite NiCo2O4 doped with graphene are highly active catalysts in the hydrogen evolution reaction (Tafel slopes = 91 mV dec−1, overpotential = 468 mV and onset potential = -339 mV), while in the oxygen evolution reaction (Tafel slopes = 51 mV dec−1, overpotential = 1752 mV and onset potential = 370 mV), bare NiCo2O4 without the addition of carbon has a worse activity (for HER: Tafel slopes = 120 mV dec−1, overpotential - does not achieve and onset potential = -404 mV, for OER: Tafel slopes = 54 mV dec−1, overpotential = 1796 mV and onset potential = 410 mV). In terms of stability, comparable results were obtained for each synthesized compound for both the HER and OER reactions.
Public health concern of antimicrobial resistance and virulence determinants in E. coli isolates from oysters in Egypt
Authors: Mohammed Rahma , Nader Sara M. , Hamza Dalia A. , Sabry Maha A.
Published: November 2024

The emergence of critical-priority E. coli, carrying a wide array of resistance and virulence factors through food sources, poses a significant challenge to public health. This study aimed to investigate the potential role of oysters sold in Egypt as a source for E. coli, identify their resistance and virulence-associated gene profiles, and assess associated zoonotic risks. A total of 33 pooled fresh oyster samples were obtained from various retail fish markets in Egypt and examined bacteriologically for the presence of E. coli. Antimicrobial resistance was performed by the disk-diffusion method, and the multiple antibiotic resistance index (MAR) was calculated. All isolates were screened for extended-spectrum beta-lactamase (ESBL) (blaTEM, blaSHV, blaCTX−M, and blaOXA−1), plasmid-mediated AmpC blaCMY−2, and carbapenemases (blaKPC, blaNDM, blaVIM, and blaOXA−48) genes by Polymerase chain reaction. Moreover, the presence of virulence-encoding genes was investigated. The virulent MDR strains were clustered using R with the pheatmap package. The prevalence of E. coli was 72.7% (24 out of 33), with 66.7% of the isolates classified as multi-drug resistant, and 75% exhibited MAR values exceeding the 0.2 threshold. Different antimicrobial sensitivity phenotypes and genotype profiles were identified in E. coli isolates. The most prevalent gene detected among all isolates was blaTEM (22/24, 91.7%). Notably, all non-ESBL producers were positive for blaCMY2. Carbapenem-resistant and carbapenem-intermediate strains were carbapenemase producers, with the predominance of the blaKPC gene (11/24, 45.8%). Remarkably, twelve out of sixteen virulence genes were identified, with papC (21/24, 87.5%) and sfa (16/24, 66.7%) genes being the most prevalent. Most isolates carry virulence genes primarily associated with extra-intestinal pathogenic E. coli (ExPEC) (87.5%) and enteropathogenic (EPEC) (70.8%) pathotypes. Four E. coli isolates exhibit cluster patterns. This study provides the first insight into the emergence of virulent MDR E. coli among oysters in Egypt. It underscores the potential role of oysters as a source for disseminating these strains within aquatic ecosystems, presenting a possible threat to public health.
Uncovering migration systems through spatio-temporal tensor co-clustering
Authors: Almquist Zack W. , Nguyen Tri Duc , Sorensen Mikael , Fu Xiao , Sidiropoulos Nicholas D.
Published: November 2024

A central problem in the study of human mobility is that of migration systems. Typically, migration systems are defined as a set of relatively stable movements of people between two or more locations over time. While these emergent systems are expected to vary over time, they ideally contain a stable underlying structure that could be discovered empirically. There have been some notable attempts to formally or informally define migration systems. However, they have been limited by being hard to operationalize and defining migration systems in ways that ignore origin/destination aspects and fail to account for migration dynamics over time. In this work, we propose to employ spatio-temporal tensor co-clustering—that stems from signal processing and machine learning theory—as a novel migration system analysis tool. Tensor co-clustering is designed to cluster entities exhibiting similar patterns across multiple modalities and thus suits our purpose of analyzing spatial migration activities across time. To demonstrate its effectiveness in describing stable migration systems, we first focus on domestic migration between counties in the US from 1990 to 2018. We conduct three case studies on domestic migration, namely, (i) US Metropolitan Areas, (ii) the state of California, and (iii) Louisiana, in which the last focuses on detecting exogenous events such as Hurricane Katrina in 2005. In addition, we also examine a case study at a larger scale, using worldwide international migration data from 200 countries between 1990 and 2015. Finally, we conclude with a discussion of this approach and its limitations.
Event Horizon Telescope observations exclude compact objects in baseline mimetic gravity
Authors: Khodadi Mohsen , Vagnozzi Sunny , Firouzjaee Javad T.
Published: November 2024

Mimetic gravity has gained significant appeal in cosmological contexts, but static spherically symmetric space-times within the baseline theory are highly non-trivial: the two natural solutions are a naked singularity and a black hole space-time obtained through an appropriate gluing procedure. We study the shadow properties of these two objects, finding both to be pathological. In particular, the naked singularity does not cast a shadow, whereas the black hole casts a shadow which is too small. We argue that the Event Horizon Telescope images of M87$$^{\star }$$ and Sgr A$$^{\star }$$ rule out the baseline version of mimetic gravity, preventing the theory from successfully accounting for the dark sector on cosmological scales. Our results highlight an interesting complementarity between black hole imaging observations and modified gravity theories of cosmological interest.
Effect of NK cell receptor genetic variation on allogeneic stem cell transplantation outcome and in vitro NK cell cytotoxicity
Authors: Nihtilä Julia , Penna Leena , Salmenniemi Urpu , Itälä-Remes Maija , Crossland Rachel E. , Gallardo David , Bogunia-Kubik Katarzyna , Lacina Piotr , Bieniaszewska Maria , Giebel Sebastian , Karjalainen Katariina , Jahan Farhana , Kerkelä Erja , Hyvärinen Kati , Koskela Satu , Ritari Jarmo , Partanen Jukka
Published: November 2024

Natural killer (NK) cells recognize and may kill malignant cells via their cell surface receptors. Killer cell immunoglobulin-like receptor (KIR) genotypes of donors have been reported to adjust the risk of relapse after allogeneic stem cell transplantation (HSCT), particularly in patients with acute myeloid leukemia. To test whether non-KIR NK cell receptors have a similar effect, we screened 1,638 genetic polymorphisms in 21 non-KIR NK cell receptor genes for their associations with relapse and graft-versus-host disease (GVHD) after HSCT in 1,491 HSCT donors (from Finland, the UK, Spain, and Poland), divided into a discovery and replication cohort. Eleven polymorphisms regulating or located in CD226, CD244, FCGR3A, KLRD1, NCR3, and PVRIG were associated with the risks for relapse and GVHD. These associations could not be confirmed in the replication cohort. Blood donor NK cells carrying alleles showing genetic protection for relapse had a higher in vitro NK cell killing activity than non-carriers whereas those with alleles genetically protective for GVHD had lower cytotoxicity, potentially indicating functional effects. Taken together, these results show no robust effects of genetic variation in the tested non-KIR NK cell receptors on the outcome of HSCT.
Mutational signature analyses in multi-child families reveal sources of age-related increases in human germline mutations
Authors: Shojaeisaadi Habiballah , Schoenrock Andrew , Meier Matthew J. , Williams Andrew , Norris Jill M. , Palmer Nicholette D. , Yauk Carole L. , Marchetti Francesco
Published: November 2024

Whole-genome sequencing studies of parent–offspring trios have provided valuable insights into the potential impact of de novo mutations (DNMs) on human health and disease. However, the molecular mechanisms that drive DNMs are unclear. Studies with multi-child families can provide important insight into the causes of inter-family variability in DNM rates but they are highly limited. We characterized 2479 de novo single nucleotide variants (SNVs) in 13 multi-child families of Mexican-American ethnicity. We observed a strong paternal age effect on validated de novo SNVs with extensive inter-family variability in the yearly rate of increase. Children of older fathers showed more C > T transitions at CpG sites than children from younger fathers. Validated SNVs were examined against one cancer (COSMIC) and two non-cancer (human germline and CRISPR-Cas 9 knockout of human DNA repair genes) mutational signature databases. These analyses suggest that inaccurate DNA mismatch repair during repair initiation and excision processes, along with DNA damage and replication errors, are major sources of human germline de novo SNVs. Our findings provide important information for understanding the potential sources of human germline de novo SNVs and the critical role of DNA mismatch repair in their genesis.
Kinetic inductance current sensor for visible to near-infrared wavelength transition-edge sensor readout
Authors: Szypryt Paul , Bennett Douglas A. , Fogarty Florang Ian , Fowler Joseph W. , Giachero Andrea , Hummatov Ruslan , Lita Adriana E. , Mates John A. B. , Nam Sae Woo , O’Neil Galen C. , Swetz Daniel S. , Ullom Joel N. , Vissers Michael R. , Wheeler Jordan , Gao Jiansong
Published: November 2024

Single-photon detectors based on the superconducting transition-edge sensor are used in a number of visible to near-infrared applications, particularly for photon-number-resolving measurements in quantum information science. To be practical for large-scale spectroscopic imaging or photonic quantum computing applications, the size of visible to near-infrared transition-edge sensor arrays and their associated readouts must be increased from a few pixels to many thousands. In this manuscript, we introduce the kinetic inductance current sensor, a scalable readout technology that exploits the nonlinear kinetic inductance in a superconducting resonator to make sensitive current measurements. Kinetic inductance current sensors can replace superconducting quantum interference devices for many applications because of their ability to measure fast, high slew-rate signals, their compatibility with standard microwave frequency-division multiplexing techniques, and their relatively simple fabrication. Here, we demonstrate the readout of a visible to near-infrared transition-edge sensor using a kinetic inductance current sensor with 3.7 MHz of bandwidth. We measure a readout noise of $$1.4\,{{{\rm{pA}}}}/\sqrt{{{{\rm{Hz}}}}}$$
1.4

pA
/

Hz

, considerably below the detector noise at frequencies of interest, and an energy resolution of (0.137 ± 0.001) eV at 0.8 eV, comparable to resolutions observed with non-multiplexed superconducting quantum interference device readouts.
Antibiotic resistance mediated by gene amplifications
Authors: Silva Kalinga Pavan T. , Khare Anupama
Published: November 2024

Apart from horizontal gene transfer and sequence-altering mutational events, antibiotic resistance can emerge due to the formation of tandem repeats of genomic regions. This phenomenon, also known as gene amplification, has been implicated in antibiotic resistance in both laboratory and clinical scenarios, where the evolution of resistance via amplifications can affect treatment efficacy. Antibiotic resistance mediated by gene amplifications is unstable and consequently can be difficult to detect, due to amplification loss in the absence of the selective pressure of the antibiotic. Further, due to variable copy numbers in a population, amplifications result in heteroresistance, where only a subpopulation is resistant to an antibiotic. While gene amplifications typically lead to resistance by increasing the expression of resistance determinants due to the higher copy number, the underlying mechanisms of resistance are diverse. In this review article, we describe the various pathways by which gene amplifications cause antibiotic resistance, from efflux and modification of the antibiotic, to target modification and bypass. We also discuss how gene amplifications can engender resistance by alternate mutational outcomes such as altered regulation and protein structure, in addition to just an increase in copy number and expression. Understanding how amplifications contribute to bacterial survival following antibiotic exposure is critical to counter their role in the rise of antimicrobial resistance.
Potential drivers of urban green space availability in Latin American cities
Authors: Bakhtsiyarava Maryia , Moran Mika , Ju Yang , Zhou Yuquan , Rodriguez Daniel A. , Dronova Iryna , de Fatima Rodrigues Pereira de Pina Maria , de Matos Vanderlei Pascoal , Skaba Daniel Albert
Published: November 2024

Urban green spaces play a critical role in regulating air temperature, reducing air pollution and enhancing people’s well being. Yet, existing data and research on potential drivers of urban green space availability in Latin America are limited. Here, focusing on 371 large cities in 11 countries in Latin America, we described the total and per capita variability of urban green space, its spatial configuration and green urban parks across the categories of cities’ natural, built and socioeconomic environments. We tested the relative importance of geographic (climate) versus city-level built environment (population, population density, street intersection density) and socioeconomic (city gross domestic product per capita, unemployment, education) drivers in explaining urban green space availability. We found a high level of heterogeneity in green space quantity across cities and across categories of cities’ environments. Relative to other city factors, climate zone had the largest influence in explaining the quantity of green space, whereas education, street intersection density and population density were the most important drivers of urban park availability. The significance of climate for green space availability, combined with the inequitable quantity of green space, indicates that cities have differing capacities to implement nature-based solutions for heat mitigation and health promotion.
Impact of photobleaching on quantitative, spatio-temporal, super-resolution imaging of mitochondria in live C. elegans larvae
Authors: Ioannis Segos , Jens Van Eeckhoven , Alan Greig , Michael Redd , Christopher Thrasivoulou , Barbara Conradt
Published: November 2024

Super-resolution (SR) 3D rendering allows superior quantitative analysis of intracellular structures but has largely been limited to fixed or ex vivo samples. Here we developed a method to perform SR live imaging of mitochondria during post-embryonic development of C. elegans larvae. Our workflow includes the drug-free mechanical immobilisation of animals using polystyrene nanobeads, which has previously not been used for in vivo SR imaging. Based on the alignment of moving objects and global threshold-based image segmentation, our method enables an efficient 3D reconstruction of individual mitochondria. We demonstrate for the first time that the frequency distribution of fluorescence intensities is not affected by photobleaching, and that global thresholding alone enables the quantitative comparison of mitochondria along timeseries. Our composite approach significantly improves the study of biological structures and processes in SR during C. elegans post-embryonic development. Furthermore, the discovery that image segmentation does not require any prior correction against photobleaching, a fundamental problem in fluorescence microscopy, will impact experimental strategies aimed at quantitatively studying the dynamics of organelles and other intracellular compartments in any biological system.
Stochastically structured illumination microscopy scan less super resolution imaging
Authors: Fusco Denzel , Xypakis Emmanouil , Gigante Ylenia , Mautone Lorenza , Di Angelantonio Silvia , Ponsi Giorgia , Ruocco Giancarlo , Leonetti Marco
Published: November 2024

In super-resolution, a varying illumination image stack is required. This enriched dataset typically necessitates precise mechanical control and micron-scale optical alignment and repeatability. Here, we introduce a novel methodology for super-resolution microscopy called stochastically structured illumination microscopy (S2IM), which bypasses the need for illumination control exploiting instead the random, uncontrolled movement of the target object. We tested our methodology within the clinically relevant ophthalmoscopic setting, harnessing the inherent saccadic motion of the eye to induce stochastic displacement of the illumination pattern on the retina. We opted to avoid human subjects by utilizing a phantom eye model featuring a retina composed of human induced pluripotent stem cells (iPSC) retinal neurons and replicating the ocular saccadic movements by custom actuators. Our findings demonstrate that S2IM unlocks scan-less super-resolution with a resolution enhancement of 1.91, with promising prospects also beyond ophthalmoscopy applications such as active matter or atmospheric/astronomical observation.
Towards next-gen smart manufacturing systems: the explainability revolution
Authors: Abhilash Puthanveettil Madathil , Luo Xichun , Liu Qi , Madarkar Rajeshkumar , Walker Charles
Published: November 2024

The paper shares the author’s perspectives on the role of explainable-AI in the evolving landscape of AI-driven smart manufacturing decisions. First, critical perspectives on the reasons for the slow adoption of explainable-AI in manufacturing are shared, leading to a discussion on its role and relevance in inspiring scientific understanding and discoveries towards achieving complete autonomy. Finally, to standardize explainability quantification, a new Transparency–Cohesion–Comprehensibility (TCC) evaluation framework is proposed and demonstrated.
Introduction to Polymer Complexes
Authors: Kuzume A. , Yamamoto K.
Published: November 2024

Polymer complexes have been increasingly applied in various fields and are attracting increasing interest as a new material system. Polymers typically include synthetic resins, synthetic fibers, and proteins, and generally exhibit functionality due to their higher-order structure, light weight, excellent formability, and unique optical and electromagnetic properties. On the other hand, metal complexes are a group of substances that have a structure consisting of a metal bonded to a ligand through coordination bonds, covalent bonds, hydrogen bonds, van der Waals forces, etc., and have various functions, such as electron transport properties, optical properties, and electrocatalytic properties. Therefore, polymer complexes, which are combinations of polymers and metal complexes, are expected to be a group of materials with various physical functions and chemical properties. Such properties and functions include steric effects, local effects, etc., and a clear understanding of their complex structure, properties, and functions is important for their further development. This chapter provides an overview of the history, classification, characteristics, and functions of polymer complexes.
Helical Polymer Complexes
Authors: Akine S.
Published: November 2024

This chapter describes the synthesis, structural features, and properties of polymer–metal complexes with various helical structures. Metal-containing helical structures can be obtained either by complexation of a pre-formed organic oligomer/polymer ligand with metal ions or by simultaneous formation of the oligomer/polymer main chain and the helical structure by metal complexation. In the first strategy, flexible linear oligomer/polymer molecules, such as bipyridine oligomers, are used to obtain self-assembled metal helicates with double and triple helical structures. The unique helical structures are based primarily on the well-defined coordination structures of the metal complex motifs. In addition, coordination bonds are used to form base pairs of DNA double helices instead of conventional hydrogen bonds. Single helical structures, such as metallo-foldamers, can also be obtained by metal complexation of linear oligomeric molecules. In the second strategy, oligomeric metal complexes with single and double helical structures are obtained by helically assembling small subunits by coordination bonds. In this case, metal complexation simultaneously leads to elongation of the main chain and formation of a helical structure. Helical metal complexes generally have dynamic features due to the reversibility of the coordination bonds. By exploiting these dynamic properties, various types of stimuli-responsive structural conversions have been achieved.
Metallosupramolecular Polymers as Display Materials
Authors: Higuchi M.
Published: November 2024

This chapter introduces metallosupramolecular polymers (MSPs) as electrochromic (EC) display materials. MSPs are synthesized by the complexation of metal ions and multitopic organic ligands. MSPs with metal-to-ligand charge transfer (MLCT) absorption show reversible EC changes by electrochemical redox of the metal species. MSPs with one-, two- and three-dimensional structures show different EC properties. EC devices with MSPs have also been fabricated successfully by combination with an electrolyte layer and a counter material layer.
Polymer-protected Nanoparticle Materials
Authors: Kambe T. , Yamamoto K.
Published: November 2024

The use of dendrimers, which do not have a molecular weight distribution, enables controlled accumulation of metal ions in controlled numbers. These polymer complexes have recently been attracting attention due to their ability to utilize the accumulated metal ions for the synthesis of nanosized to sub-nanosized particles. In particular, the number of metals to be accumulated in a phenylazomethine dendrimer template system can be specified, which makes it possible to selectively synthesize clusters with a specific number of metals. This enables the appearance of new physical properties of sub-nanosized metal particles, which have been an unexplored material group until now, and these particles are beginning to attract attention mainly for their high catalytic activity. Nanoparticles and clusters, despite their specific functions, cannot be used due to stability problems. The protection of such nanoparticles with polymers enables their application as polymer complex materials. In this chapter, we describe the synthesis of polymer-protected nanoparticles and clusters and their application as catalysts with a focus on metal clusters using dendrimers as templates.
A stimulus responsive microneedle-based drug delivery system for cancer therapy
Authors: Tang Hongyu , Cheng Xueqing , Liang Ling , Chen Bo Zhi , Liu Chaoyong , Wang Yushu
Published: November 2024

Based on the tumor microenvironment and the advantages of microneedle administration, we summarize the application of responsive microneedles in cancer treatment, providing a reference for the research of drug delivery systems in cancer treatment.
Synthesis of environmentally friendly energetic cocrystal derived from commodity chemicals
Authors: Inoue Kazuki , Nishiwaki Yosuke , Kumasaki Mieko , Matsumoto Shinya , Okada Ken
Published: November 2024

Ammonium nitrate/glycine (2 : 1) energetic cocrystal was synthesized to address two drawbacks of ammonium nitrate: phase transitions and hygroscopicity. The cocrystal did not show phase transitions and exhibited decreased hygroscopicity.
Activating FeMoO4 nanosheet arrays by partial nickel substitution for efficient electrocatalytic seawater oxidation
Authors: Gao Jun-Ya , Ma Yin-Lei , Qian Guang-Sheng , Si Meng-Ying , Han Ling-Li , Li Ji-Sen
Published: November 2024

Nickel is integrated into self-supported FeMoO4 nanosheet arrays by a spontaneous redox reaction, which shows significantly enhanced electrocatalytic OER performance and long-term durability under both alkaline and alkaline seawater conditions.
Zero-dimensional organic–inorganic hybrid zinc halide with stable broadband blue light emissions
Authors: Zhang Jie , Ma Yu-Xin , Wu Ming , He Qing , Chen Shuya , Ju Ping , He Yuan-Chun , Lei Xiaowu
Published: November 2024

A series of zero-dimensional zinc halide materials based on [ZnX4]2− tetrahedra are prepared, which exhibit intense broadband blue light emission.
Substituent effects on the photophysics of the kaede chromophore
Authors: Fatima Anam , Bressan Giovanni , Ashworth Eleanor K. , Page Philip C. B. , Bull James N. , Meech Stephen R.
Published: November 2024

Ultrafast time resolved spectroscopy probes substituent dependent photophysics of the kaede fluorescent protein chromophore.
Insight into the influence of Re and Cl on Ag catalysts in ethylene epoxidation
Authors: Keijzer Claudia J. , Weide Pim T. , Helfferich Kristiaan H. , Zieciak Justyna , de Ridder Marco , Dalebout Remco , Lohr Tracy L. , Lockemeyer John R. , van den Brink Peter , de Jongh Petra E.
Published: November 2024

Crystalline AgReO4 was formed in Re-promoted Ag catalysts. The effect of Re on catalysis and EO isomerization was tested without and with the industrially relevant ethyl chloride. EO isomerization was greatly affected by both Re and Cl.
An electric double layer regulator empowers a robust solid–electrolyte interphase for potassium metal batteries
Authors: Lian Xueyu , Xu Liang , Ju Zhijin , Chen Ziang , Chen Xiaopeng , Yi Yuyang , Tian Zhengnan , Cheng Tao , Dou Shixue , Tao Xinyong , Sun Jingyu
Published: November 2024

A versatile separator modification strategy is proposed to rearrange anode interface species, realizing a robust inorganic-rich solid–electrolyte interphase thus ensuring a durable potassium metal batteries.
Domestic groundwater wells in Appalachia show evidence of low-dose, complex mixtures of legacy pollutants
Authors: Bugher Nicolette A. , Xiong Boya , Gentles Runako I. , Glist Lukas D. , Siegel Helen G. , Johnson Nicholaus P. , Clark Cassandra J. , Deziel Nicole C. , Saiers James E. , Plata Desiree L.
Published: November 2024

Private groundwater wells in communities co-located with historically contaminated sites and ongoing industrial activity contain complex mixtures of low-dose organic chemicals.
Combating eukaryotic and prokaryotic harmful algal blooms with visible-light driven BiOBrxI1−x/MFe2O4/g-C3N4 (M = Co & Ni) recyclable photocatalysts
Authors: A Anjitha , K Shijina , K. V. Ajayan , Swaminathan Sindhu , Lo Irene M. C. , Sridharan Kishore
Published: November 2024

Visible light driven degradation of harmful algal blooms in the presence of synthesized heterojunction photocatalysts showcasing their complete rupture and the photocatalyst's superior efficiency and recyclability is demonstrated in this study.
A novel method for exploration and prediction of the bioactive target of rice bran-derived peptide (KF-8) by integrating computational methods and experiments
Authors: Liang Rui , Song Fangliang , Liang Ying , Fang Yanpeng , Wang Jianqiang , Chen Yajuan , Chen Zhongxu , Tan Xiaorong , Dong Jie
Published: November 2024

The diagram of the strategy to explore peptide targets based on model predictions and experiments.
Crystalline/amorphous c-NiMo/a-NiMoOx nanoarrays for urea-assisted energy-saving H2 production in alkaline seawater
Authors: Guo Dongxue , Ping Yi , Wang Chuanjiao , Hou Changan , Wang Danhong
Published: November 2024

Electrocatalytic seawater splitting is regarded as the most effective method for producing green hydrogen (H2), replacing sluggish oxygen evolution reaction (OER) with thermodynamically favorable urea oxidation reaction (UOR) would enable energy-saving and chlorine-free H2 production.
Photocatalytic deposition of noble metals on 0D, 1D, and 2D TiO2 structures: a review
Authors: Veziroglu Salih , Shondo Josiah , Tjardts Tim , Sarwar Tamim B. , Sünbül Ayse , Mishra Yogendra Kumar , Faupel Franz , Aktas Oral Cenk
Published: November 2024

In recent years, extensive research on noble metal–TiO2 nanocomposites has demonstrated their crucial role in various applications such as water splitting, self-cleaning, CO2 reduction, and wastewater treatment.
Unraveling energetics and states of adsorbing oxygen species with MoS2 for modulated work function
Authors: Yan Hejin , Chen Hongfei , Cui Xiangyue , Guan Qiye , Wang Bowen , Cai Yongqing
Published: November 2024

Oxygen doping on MoS2 provides a promising method for sulfur vacancy healing, carrier mass controlling, contact resistance reduction, and anchoring of surface electron dopants.
MnO2 nanoparticles supported on graphitic carbon nitride as an electrocatalyst for oxygen reduction and evolution
Authors: Zabielaitė Aušrinė , Kepenienė Virginija , Šimkūnaitė Dijana , Stagniūnaitė Raminta , Jasulaitienė Vitalija , Stalnionis Giedrius , Vaičiūnienė Jūratė , Tamašauskaitė-Tamašiūnaitė Loreta , Norkus Eugenijus
Published: November 2024

The use of g-CN/C as a substrate for MnO2 has been demonstrated to enhance the electrocatalytic activity of the ORR and OER.
Low carbon-to-metal ratio and nucleation of hexagonal moiré superlattices in onion-like graphitic-domains within the walls of carbon nanotubes by the pyrolysis of ferrocene in viscous boundary layers
Authors: Boi Filippo S. , Zhang Lin , Guo Xilong , Guo Jian , Wu Hansong , Wang Shanling
Published: November 2024

The original data supporting this article can be obtained from the corresponding author upon request.
Cr2TiC2Tx MXene as an adsorbent material in ultrasonic-assisted d-μ-solid phase extraction for trace detection of heavy metals
Authors: Bagheri Saman , Khurana Rashmeet Kaur , Kholil Md. Ibrahim , Loes Michael J. , Luo Shengyuan , Sinitskii Alexander
Published: November 2024

Cr2TiC2Tx MXene was used as an adsorbent for the trace determination of heavy metals in food samples, with LOD values of 0.09 and 1.9 ng mL−1, and dynamic ranges of 0.3–90 and 6–120 μg L−1 for cadmium and lead ions, respectively.
Structure, humidity adaptivity, and elasticity of hydrogen-bonded complexes formed by self-assembly of a triblock copolymer and a homopolymer
Authors: Wang Weijie , Jian Hanxin , Huang Hao , Feng Fengfeng , Meng Qingye , Li Yuli , Chen Gang , Yang Shuguang
Published: November 2024

The tri-block copolymer polystyrene-b-poly(ethylene oxide)-b-polystyrene (SES) and the homopolymer poly(acrylic acid) (PAA) were applied to fabricate elastomers with multi-hierarchical architectures.
Ultrathin 2D NiCo-MOF bimetallic nanosheets as single-atom catalysts for chemoselective hydrogenation of nitroarenes
Authors: Zhang Yu-Xuan , Ma Yi-Jie , Zhao Yu-Jia , Wang Zi-Yan , Yu Cai-Xia , Li Xiao-Qiang , Liu Lei-Lei
Published: November 2024

A 2D NiCo-MOF bimetallic nanosheet was constructed as a single-atom catalyst and it exhibited excellent performance for the hydrogenation of various nitroarenes and aldehyde compounds, in terms of high conversion, high selectivity and rapid kinetics.
Ionic-liquid/metal–organic-framework composites: synthesis and emerging sustainable applications
Authors: Zhu Maiyong
Published: November 2024

This review represents the sustainable applications of ionic liquid/metal organic framework composites.
Naphthalene diimide-based crystalline hybrid photochromic materials: structural types, photochromic mechanism, and applications
Authors: Li Li , Zeng Jian-Ge , Zhang Ning-Ning , Yu Yang-Tao , Li Shu-Hao , Hua Yang
Published: November 2024

This review summarizes recent advances in naphthalene diimide-based crystalline hybrid photochromic materials, including the different structures types, photochromic mechanism and their applications in this field.
N-doped carbon quantum dots for the selective detection of OCl− ions, bioimaging, and the production of Fe3O4 nanoparticles utilized in the synthesis of substituted imidazole
Authors: Hota Namrata Priyadarshini , Kulathu Iyer Sathiyanarayanan
Published: November 2024

Nitrogen-doped quantum dots (NCQD) were synthesized by solvothermal means using o-phenylenediamine and l-tartaric acid.
Dilute nanocomposites for capacitive energy storage: progress, challenges and prospects
Authors: Li Li , Xu Wenhan , Rui Guanchun , Zhang Shixian , Zhang Q. M. , Wang Qing
Published: November 2024

This perspective highlights the unconventional phenomena in dilute nanocomposites that break multiple classic theories in dielectrics, holding promise for achieving unprecedentedly high capacitive energy density in polymer dielectrics.