bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phasor-FSTM: a new paradigm for multicolor super-resolution imaging of living cells based on fluorescence modulation and lifetime multiplexing
Authors: Wang Luwei , Chen Yue , Guo Jiaqing , Weng Xiaoyu , Yan Wei , Song Jun , Ye Tong , Qu Junle 
Published: January 2025

AbstractMulticolor microscopy and super-resolution optical microscopy are two widely used techniques that greatly enhance the ability to distinguish and resolve structures in cellular imaging. These methods have individually transformed cellular imaging by allowing detailed visualization of cellular and subcellular structures, as well as organelle interactions. However, integrating multicolor and super-resolution microscopy into a single method remains challenging due to issues like spectral overlap, crosstalk, photobleaching, phototoxicity, and technical complexity. These challenges arise from the conflicting requirements of using different fluorophores for multicolor labeling and fluorophores with specific properties for super-resolution imaging. We propose a novel multicolor super-resolution imaging method called phasor-based fluorescence spatiotemporal modulation (Phasor-FSTM). This method uses time-resolved detection to acquire spatiotemporal data from encoded photons, employs phasor analysis to simultaneously separate multiple components, and applies fluorescence modulation to create super-resolution images. Phasor-FSTM enables the identification of multiple structural components with greater spatial accuracy on an enhanced laser scanning confocal microscope using a single-wavelength laser. To demonstrate the capabilities of Phasor-FSTM, we performed two-color to four-color super-resolution imaging at a resolution of ~λ/5 and observed the interactions of organelles in live cells during continuous imaging for a duration of over 20 min. Our method stands out for its simplicity and adaptability, seamlessly fitting into existing laser scanning microscopes without requiring multiple laser lines for excitation, which also provides a new avenue for other super-resolution imaging technologies based on different principles to build multi-color imaging systems with the requirement of a lower budget.
The molecular reach of antibodies crucially underpins their viral neutralisation capacity
Authors: Huhn Anna , Nissley Daniel , Wilson Daniel B. , Kutuzov Mikhail A. , Donat Robert , Tan Tiong Kit , Zhang Ying , Barton Michael I. , Liu Chang , Dejnirattisai Wanwisa , Supasa Piyada , Mongkolsapaya Juthathip , Townsend Alain , James William , Screaton Gavin , van der Merwe P. Anton , Deane Charlotte M. , Isaacson Samuel A. , Dushek Omer 
Published: January 2025

AbstractKey functions of antibodies, such as viral neutralisation, depend on high-affinity binding. However, viral neutralisation poorly correlates with antigen affinity for reasons that have been unclear. Here, we use a new mechanistic model of bivalent binding to study >45 patient-isolated IgG1 antibodies interacting with SARS-CoV-2 RBD surfaces. The model provides the standard monovalent affinity/kinetics and new bivalent parameters, including the molecular reach: the maximum antigen separation enabling bivalent binding. We find large variations in these parameters across antibodies, including reach variations (22–46 nm) that exceed the physical antibody size (~15 nm). By using antigens of different physical sizes, we show that these large molecular reaches are the result of both the antibody and antigen sizes. Although viral neutralisation correlates poorly with affinity, a striking correlation is observed with molecular reach. Indeed, the molecular reach explains differences in neutralisation for antibodies binding with the same affinity to the same RBD-epitope. Thus, antibodies within an isotype class binding the same antigen can display differences in molecular reach, substantially modulating their binding and functional properties.
Global and regional perspectives on optimizing thermo-responsive dynamic windows for energy-efficient buildings
Authors: Gao Yuan , Jonsson Jacob C. , Curcija D. Charlie , Vidanovic Simon , Hong Tianzhen 
Published: January 2025

AbstractArchitectural thermo-responsive dynamic windows offer an autonomous solution for solar heat regulation, thereby reducing building energy consumption. Previous work has emphasized the significance of thermo-responsive windows in hot climates due to their role in solar heat control and subsequent energy conservation; conversely, our study provides a different perspective. Through a global-scale analysis, we explore over 100 material samples and execute more than 2.8 million simulations across over two thousand global locations. World heatmap results, derived from well-trained artificial neural network models, reveal that thermo-responsive windows are especially useful in climates where buildings demand both heating and cooling energy, whereas thermo-responsive windows with optimal transition temperatures show no dynamic features in most of low-latitude tropical regions. Additionally, this study provides a practical guideline and an open-source mapping tool to optimize the intrinsic properties of thermo-responsive materials and evaluate their energy performance for sustainable buildings at various geographical scales.
On the longevity and inherent hermeticity of silicon-ICs: evaluation of bare-die and PDMS-coated ICs after accelerated aging and implantation studies
Authors: Nanbakhsh Kambiz , Shah Idil Ahmad , Lamont Callum , Dücső Csaba , Akgun Ömer Can , Horváth Domonkos , Tóth Kinga , Meszéna Domokos , Ulbert István , Mazza Federico , Constandinou Timothy G. , Serdijn Wouter , Vanhoestenberghe Anne , Donaldson Nick , Giagka Vasiliki 
Published: January 2025

Abstract
Silicon integrated circuits (ICs) are central to the next-generation miniature active neural implants, whether packaged in soft polymers for flexible bioelectronics or implanted as bare die for neural probes. These emerging applications bring the IC closer to the corrosive body environment, raising reliability concerns, particularly for chronic use. Here, we evaluate the inherent hermeticity of bare die ICs, and examine the potential of polydimethylsiloxane (PDMS), a moisture-permeable elastomer, as a standalone encapsulation material. For this aim, the electrical and material performance of ICs sourced from two foundries was evaluated through one-year accelerated in vitro and in vivo studies. ICs featured custom-designed test structures and were partially PDMS coated, creating two regions on each chip, uncoated “bare die” and “PDMS-coated”. During the accelerated in vitro study, ICs were electrically biased and periodically monitored. Results revealed stable electrical performance, indicating the unaffected operation of ICs even when directly exposed to physiological fluids. Despite this, material analysis revealed IC degradation in the bare regions. PDMS-coated regions, however, revealed limited degradation, making PDMS a suitable IC encapsulant for years-long implantation. Based on the new insights, guidelines are proposed that may enhance the longevity of implantable ICs, broadening their applications in the biomedical field.
Comparative 3D ultrastructure of Plasmodium falciparum gametocytes
Authors: Evers Felix , Roverts Rona , Boshoven Cas , Kea-te Lindert Mariska , Verhoef Julie M. J. , Sommerdijk Nico , Sinden Robert E. , Akiva Anat , Kooij Taco W. A. 
Published: January 2025

AbstractDespite the enormous significance of malaria parasites for global health, some basic features of their ultrastructure remain obscure. Here, we apply high-resolution volumetric electron microscopy to examine and compare the ultrastructure of the transmissible male and female sexual blood stages of Plasmodium falciparum as well as the more intensively studied asexual blood stages revisiting previously described phenomena in 3D. In doing so, we challenge the widely accepted notion of a single mitochondrion by demonstrating the presence of multiple mitochondria in gametocytes. We also provide evidence for a gametocyte-specific cytostome, or cell mouth. Furthermore, we generate the first 3D reconstructions of the parasite’s endoplasmic reticulum (ER) and Golgi apparatus as well as gametocyte-induced extraparasitic structures in the infected red blood cell. Assessing interconnectivity between organelles, we find frequent structural appositions between the nucleus, mitochondria, and apicoplast. We provide evidence that the ER is a promiscuous interactor with numerous organelles and the trilaminar pellicle of the gametocyte. Public availability of these volumetric electron microscopy resources will facilitate reinterrogation by others with different research questions and expertise. Taken together, we reconstruct the 3D ultrastructure of P. falciparum gametocytes at nanometre scale and shed light on the unique organellar biology of these deadly parasites.
Overlapping qubits from non-isometric maps and de Sitter tensor networks
Authors: Cao ChunJun , Chemissany Wissam , Jahn Alexander , Zimborás Zoltán 
Published: January 2025

AbstractThe emergence of a local effective theory from a more fundamental theory of quantum gravity with seemingly fewer degrees of freedom is a major puzzle of theoretical physics. A recent approach to this problem is to consider general features of the Hilbert space maps relating these theories. In this work, we construct approximately local observables, or overlapping qubits, from such non-isometric maps. We show that local processes in effective theories can be spoofed with a quantum system with fewer degrees of freedom, with deviations from actual locality identifiable as features of quantum gravity. For a concrete example, we construct two tensor network models of de Sitter space-time, demonstrating how exponential expansion and local physics can be spoofed for a long period before breaking down. Our results highlight the connection between overlapping qubits, Hilbert space dimension verification, degree-of-freedom counting in black holes, holography, and approximate locality in quantum gravity.
Long non-coding RNAs direct the SWI/SNF complex to cell type-specific enhancers
Authors: Oo James A. , Warwick Timothy , Pálfi Katalin , Lam Frederike , McNicoll Francois , Prieto-Garcia Cristian , Günther Stefan , Cao Can , Zhou Yinuo , Gavrilov Alexey A. , Razin Sergey V. , Cabrera-Orefice Alfredo , Wittig Ilka , Pullamsetti Soni Savai , Kurian Leo , Gilsbach Ralf , Schulz Marcel H. , Dikic Ivan , Müller-McNicoll Michaela , Brandes Ralf P. , Leisegang Matthias S. 
Published: January 2025

AbstractThe coordination of chromatin remodeling is essential for DNA accessibility and gene expression control. The highly conserved and ubiquitously expressed SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex plays a central role in cell type- and context-dependent gene expression. Despite the absence of a defined DNA recognition motif, SWI/SNF binds lineage specific enhancers genome-wide where it actively maintains open chromatin state. It does so while retaining the ability to respond dynamically to cellular signals. However, the mechanisms that guide SWI/SNF to specific genomic targets have remained elusive. Here we demonstrate that trans-acting long non-coding RNAs (lncRNAs) direct the SWI/SNF complex to cell type-specific enhancers. SWI/SNF preferentially binds lncRNAs and these predominantly bind DNA targets in trans. Together they localize to enhancers, many of which are cell type-specific. Knockdown of SWI/SNF- and enhancer-bound lncRNAs causes the genome-wide redistribution of SWI/SNF away from enhancers and a concomitant differential expression of spatially connected target genes. These lncRNA-SWI/SNF-enhancer networks support an enhancer hub model of SWI/SNF genomic targeting. Our findings reveal that lncRNAs competitively recruit SWI/SNF, providing a specific and dynamic layer of control over chromatin accessibility, and reinforcing their role in mediating enhancer activity and gene expression.
Optical single-shot readout of spin qubits in silicon
Authors: Gritsch Andreas , Ulanowski Alexander , Pforr Jakob , Reiserer Andreas 
Published: January 2025

AbstractSmall registers of spin qubits in silicon can exhibit hour-long coherence times and exceeded error-correction thresholds. However, their connection to larger quantum processors is an outstanding challenge. To this end, spin qubits with optical interfaces offer key advantages: they can minimize the heat load and give access to modular quantum computing architectures that eliminate cross-talk and offer a large connectivity. Here, we implement such an efficient spin-photon interface based on erbium dopants in a nanophotonic resonator. We demonstrate optical single-shot readout of a spin in silicon whose coherence exceeds the Purcell-enhanced optical lifetime, paving the way for entangling remote spins via photon interference. As erbium dopants can emit coherent photons in the minimal-loss band of optical fibers, and tens of such qubits can be spectrally multiplexed in each resonator, the demonstrated hardware platform offers unique promise for distributed quantum information processing based on scalable, integrated silicon devices.
Dissipative Landau-Zener tunneling in the crossover regime from weak to strong environment coupling
Authors: Dai X. , Trappen R. , Chen H. , Melanson D. , Yurtalan M. A. , Tennant D. M. , Martinez A. J. , Tang Y. , Mozgunov E. , Gibson J. , Grover J. A. , Disseler S. M. , Basham J. I. , Novikov S. , Das R. , Melville A. J. , Niedzielski B. M. , Hirjibehedin C. F. , Serniak K. , Weber S. J. , Yoder J. L. , Oliver W. D. , Zick K. M. , Lidar D. A. , Lupascu A. 
Published: January 2025

AbstractLandau-Zener tunneling, which describes the transition in a two-level system during a sweep through an anti-crossing, is a model applicable to a wide range of physical phenomena. Realistic quantum systems are affected by dissipation due to coupling to their environments. An important aspect of understanding such open quantum systems is the relative energy scales of the system itself and the system-environment coupling, which distinguishes the weak- and strong-coupling regimes. Using a tunable superconducting flux qubit, we observe the crossover from weak to strong coupling to the environment in Landau-Zener tunneling. Our results confirm previous theoretical studies of dissipative Landau-Zener tunneling in the weak and strong coupling limits. We devise a spin bath model that effectively captures the crossover regime. This work is relevant for understanding the role of dissipation in quantum annealing, where the system is expected to go through a cascade of Landau-Zener transitions before reaching the target state.
Characterizing cell-type spatial relationships across length scales in spatially resolved omics data
Authors: dos Santos Peixoto Rafael , Miller Brendan F. , Brusko Maigan A. , Aihara Gohta , Atta Lyla , Anant Manjari , Atkinson Mark A. , Brusko Todd M. , Wasserfall Clive H. , Fan Jean 
Published: January 2025

AbstractSpatially resolved omics (SRO) technologies enable the identification of cell types while preserving their organization within tissues. Application of such technologies offers the opportunity to delineate cell-type spatial relationships, particularly across different length scales, and enhance our understanding of tissue organization and function. To quantify such multi-scale cell-type spatial relationships, we present CRAWDAD, Cell-type Relationship Analysis Workflow Done Across Distances, as an open-source R package. To demonstrate the utility of such multi-scale characterization, recapitulate expected cell-type spatial relationships, and evaluate against other cell-type spatial analyses, we apply CRAWDAD to various simulated and real SRO datasets of diverse tissues assayed by diverse SRO technologies. We further demonstrate how such multi-scale characterization enabled by CRAWDAD can be used to compare cell-type spatial relationships across multiple samples. Finally, we apply CRAWDAD to SRO datasets of the human spleen to identify consistent as well as patient and sample-specific cell-type spatial relationships. In general, we anticipate such multi-scale analysis of SRO data enabled by CRAWDAD will provide useful quantitative metrics to facilitate the identification, characterization, and comparison of cell-type spatial relationships across axes of interest.
Restoring small water bodies to improve lake and river water quality in China
Authors: Shen Wangzheng , Zhang Liang , Ury Emily A. , Li Sisi , Xia Biqing , Basu Nandita B. 
Published: January 2025

AbstractClimate change, population growth, and agricultural intensification are increasing nitrogen (N) inputs, while driving the loss of inland water bodies that filter excess N. However, the interplay between N inputs and water body dynamics, and its implications for water quality remain poorly understood. Analyzing data from 1995 to 2015 across China, here, we find a 71% reduction in the area of small (<104.5 m2) water bodies (SWB), primarily in high-N-input agricultural regions. Preferential loss of SWBs, the most efficient nutrient filters, places 42% of China at high water quality risk due to increasing N inputs and declining SWB density. Currently, N removal by water bodies is 986 kilotonnes year−1, but restoring 2.3 million hectares of SWB could increase removal by 21%, compared to just 5% for equivalent restoration of large water bodies. Targeted SWB restoration is crucial for improving water quality and mitigating N pollution in China.
A review of displacement cascade simulations using molecular dynamics emphasizing interatomic potentials for TPBAR components
Authors: Roy Ankit , Nandipati Giridhar , Casella Andrew M. , Senor David J. , Devanathan Ram , Soulami Ayoub 
Published: January 2025

AbstractThis review explores molecular dynamics simulations for studying radiation damage in Tritium Producing Burnable Absorber Rod (TPBAR) materials, emphasizing the role of interatomic potentials in displacement cascades. Recent machine learning potentials (MLPs), trained on quantum data, enhance prediction accuracy over traditional models like EAM. We highlight temperature, PKA energy, and composition effects on damage evolution in TPBAR components, recommending suitable potentials and discussing advancements for materials in extreme radiation environments.
Tropical cyclone risk for global ecosystems in a changing climate
Authors: Kropf Chahan M. , Vaterlaus Lisa , Bresch David N. , Pellissier Loïc 
Published: January 2025

AbstractCoastal ecosystems provide a range of services including erosion prevention, clean water provision and carbon sequestration. With climate change, the rapid change in frequency and intensity of tropical cyclones may alter the composition of the ecosystems themselves potentially degrading the services they provide. Here we classify global ecoregions into dependent, resilient and vulnerable and show that a combined 9.4% of the surface of all terrestrial ecosystems is susceptible to transformation due to cyclone pattern changes between 1980–2017 and 2015–2050 under climate scenario SSP5-8.5 using the STORM model. Even for the most resilient ecosystems already experiencing winds >60 m s−1 regularly, the average interval between two storms is projected to decrease from 19 to 12 years which is potentially close to their recovery time. Our study advocates for a shift in the consideration of the tropical cyclone impact from immediate damage to effects on long-term natural recovery cycles.
Ferrimagnetic Heusler tunnel junctions with fast spin-transfer torque switching enabled by low magnetization
Authors: Garg Chirag , Filippou Panagiotis Ch. , Ikhtiar  , Ferrante Yari , Yang See-Hun , Hughes Brian , Rettner Charles T. , Phung Timothy , Faleev Sergey , Topuria Teya , Samant Mahesh G. , Jeong Jaewoo , Parkin Stuart S. P. 
Published: January 2025

AbstractMagnetic random-access memory that uses magnetic tunnel junction memory cells is a high-performance, non-volatile memory technology that goes beyond traditional charge-based memories. Today, its speed is limited by the high magnetization of the memory storage layer. Here we prepare magnetic tunnel junction memory devices with a low magnetization ferrimagnetic Heusler alloy Mn3Ge as the memory storage layer on technologically relevant amorphous substrates using a combination of a nitride seed layer and a chemical templating layer. We switch the magnetic state of the storage layer with nanosecond long write pulses at a reliable write error rate of 10−7 and detect a tunnelling magnetoresistance of 87% at ambient temperature. These results provide a strategy towards lower write switching currents using ferrimagnetic Heusler materials and, therefore, to the scaling of high-performance magnetic random-access memories beyond those nodes possible with ferromagnetic memory layers.
Single immunization with genetically attenuated Pf∆mei2 (GA2) parasites by mosquito bite in controlled human malaria infection: a placebo-controlled randomized trial
Authors: Roozen Geert V. T. , van Schuijlenburg Roos , Hensen Annefleur D. O. , Koopman Jan Pieter R. , Lamers Olivia A. C. , Geurten Fiona J. A. , Sijtsma Jeroen C. , Baalbergen Els , Janse Jacqueline J. , Chevalley-Maurel Séverine , Naar Chanel M. , Bezemer Sascha , Kroeze Hans , van de Stadt Huybert J. F. , de Visser Bram , Meij Pauline , Tihaya Mara S. , Colstrup Emil , Iliopoulou Eva , de Bes-Roeleveld Helena M. , Wessels Els , van der Stoep M. Y. Eileen C. , Janse Chris J. , Murugan Rajagopal , Franke-Fayard Blandine M. D. , Roestenberg Meta 
Published: January 2025

Abstract
Malaria vaccines consisting of metabolically active Plasmodium falciparum (Pf) sporozoites can offer improved protection compared with currently deployed subunit vaccines. In a previous study, we demonstrated the superior protective efficacy of a three-dose regimen of late-arresting genetically attenuated parasites administered by mosquito bite (GA2-MB) compared with early-arresting counterparts (GA1-MB) against a homologous controlled human malaria infection. Encouraged by these results, we explored the potency of a single GA2-MB immunization in a placebo-controlled randomized trial. Primary outcomes were safety and tolerability, time-to-parasitemia and protective efficacy. Humoral and cellular immunological results were considered secondary outcomes. Here we report the safe administration of GA2-MB with no breakthrough malaria and sterile protection in nine of ten participants at 6 weeks after a single immunization with 50 GA2-infected mosquitoes, compared with none of five mock-immunized participants, against a homologous controlled human malaria infection. Immunization increased circulating Pf-specific polyfunctional effector memory CD4+ T cells coexpressing tumor necrosis factor and interleukin-2. This unprecedented 90% protective efficacy after a single low-dose immunization holds great promise for the potency of GA2 immunization. Future studies should demonstrate whether GA2 is similarly efficacious in pre-exposed populations and whether the favorable safety profile reported here holds up in larger groups. ClinicalTrials.gov registration: NCT05468606.