bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantum-enhanced radiometry via approximate quantum error correction
Authors: Wang W. , Chen Z.-J. , Liu X. , Cai W. , Ma Y. , Mu X. , Pan X. , Hua Z. , Hu L. , Xu Y. , Wang H. , Song Y. P. , Zou X.-B. , Zou C.-L. , Sun L. 
Published: June 2022

AbstractQuantum sensing based on exotic quantum states is appealing for practical metrology applications and fundamental studies. However, these quantum states are vulnerable to noise and the resulting quantum enhancement is weakened in practice. Here, we experimentally demonstrate a quantum-enhanced sensing scheme with a bosonic probe, by exploring the large Hilbert space of the bosonic mode and developing both the approximate quantum error correction and the quantum jump tracking approaches. In a practical radiometry scenario, we attain a 5.3 dB enhancement of sensitivity, which reaches 9.1 × 10−4 Hz−1/2 when measuring the excitation population of a receiver mode. Our results demonstrate the potential of quantum sensing with near-term quantum technologies, not only shedding new light on the quantum advantage of sensing, but also stimulating further efforts on bosonic quantum technologies.
Adjusting agricultural emissions for trade matters for climate change mitigation
Authors: Foong Adrian , Pradhan Prajal , Frör Oliver , Kropp Jürgen P. 
Published: June 2022

AbstractReducing greenhouse gas emissions in food systems is becoming more challenging as food is increasingly consumed away from producer regions, highlighting the need to consider emissions embodied in trade in agricultural emissions accounting. To address this, our study explores recent trends in trade-adjusted agricultural emissions of food items at the global, regional, and national levels. We find that emissions are largely dependent on a country’s consumption patterns and their agricultural emission intensities relative to their trading partners’. The absolute differences between the production-based and trade-adjusted emissions accounting approaches are especially apparent for major agricultural exporters and importers and where large shares of emission-intensive items such as ruminant meat, milk products and rice are involved. In relative terms, some low-income and emerging and developing economies with consumption of high emission intensity food products show large differences between approaches. Similar trends are also found under various specifications that account for trade and re-exports differently. These findings could serve as an important element towards constructing national emissions reduction targets that consider trading partners, leading to more effective emissions reductions overall.
Disease-economy trade-offs under alternative epidemic control strategies
Authors: Ash Thomas , Bento Antonio M. , Kaffine Daniel , Rao Akhil , Bento Ana I. 
Published: June 2022

AbstractPublic policy and academic debates regarding pandemic control strategies note disease-economy trade-offs, often prioritizing one outcome over the other. Using a calibrated, coupled epi-economic model of individual behavior embedded within the broader economy during a novel epidemic, we show that targeted isolation strategies can avert up to 91% of economic losses relative to voluntary isolation strategies. Unlike widely-used blanket lockdowns, economic savings of targeted isolation do not impose additional disease burdens, avoiding disease-economy trade-offs. Targeted isolation achieves this by addressing the fundamental coordination failure between infectious and susceptible individuals that drives the recession. Importantly, we show testing and compliance frictions can erode some of the gains from targeted isolation, but improving test quality unlocks the majority of the benefits of targeted isolation.
Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data
Authors: Dimitrov Daniel , Türei Dénes , Garrido-Rodriguez Martin , Burmedi Paul L. , Nagai James S. , Boys Charlotte , Ramirez Flores Ricardo O. , Kim Hyojin , Szalai Bence , Costa Ivan G. , Valdeolivas Alberto , Dugourd Aurélien , Saez-Rodriguez Julio 
Published: June 2022

AbstractThe growing availability of single-cell data, especially transcriptomics, has sparked an increased interest in the inference of cell-cell communication. Many computational tools were developed for this purpose. Each of them consists of a resource of intercellular interactions prior knowledge and a method to predict potential cell-cell communication events. Yet the impact of the choice of resource and method on the resulting predictions is largely unknown. To shed light on this, we systematically compare 16 cell-cell communication inference resources and 7 methods, plus the consensus between the methods’ predictions. Among the resources, we find few unique interactions, a varying degree of overlap, and an uneven coverage of specific pathways and tissue-enriched proteins. We then examine all possible combinations of methods and resources and show that both strongly influence the predicted intercellular interactions. Finally, we assess the agreement of cell-cell communication methods with spatial colocalisation, cytokine activities, and receptor protein abundance and find that predictions are generally coherent with those data modalities. To facilitate the use of the methods and resources described in this work, we provide LIANA, a LIgand-receptor ANalysis frAmework as an open-source interface to all the resources and methods.
Expanding the active charge carriers of polymer electrolytes in lithium-based batteries using an anion-hosting cathode
Authors: Sun Zongjie , Xi Kai , Chen Jing , Abdelkader Amor , Li Meng-Yang , Qin Yuanyuan , Lin Yue , Jiang Qiu , Su Ya-Qiong , Vasant Kumar R. , Ding Shujiang 
Published: June 2022

AbstractIonic-conductive polymers are appealing electrolyte materials for solid-state lithium-based batteries. However, these polymers are detrimentally affected by the electrochemically-inactive anion migration that limits the ionic conductivity and accelerates cell failure. To circumvent this issue, we propose the use of polyvinyl ferrocene (PVF) as positive electrode active material. The PVF acts as an anion-acceptor during redox processes, thus simultaneously setting anions and lithium ions as effective charge carriers. We report the testing of various Li||PVF lab-scale cells using polyethylene oxide (PEO) matrix and Li-containing salts with different anions. Interestingly, the cells using the PEO-lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) solid electrolyte deliver an initial capacity of 108 mAh g−1 at 100 μA cm−2 and 60 °C, and a discharge capacity retention of 70% (i.e., 70 mAh g−1) after 2800 cycles at 300 μA cm−2 and 60 °C. The Li|PEO-LiTFSI|PVF cells tested at 50 μA cm−2 and 30 °C can also deliver an initial discharge capacity of around 98 mAh g−1 with an electrolyte ionic conductivity in the order of 10−5 S cm−1.
Mechanically active integrins target lytic secretion at the immune synapse to facilitate cellular cytotoxicity
Authors: Wang Mitchell S. , Hu Yuesong , Sanchez Elisa E. , Xie Xihe , Roy Nathan H. , de Jesus Miguel , Winer Benjamin Y. , Zale Elizabeth A. , Jin Weiyang , Sachar Chirag , Lee Joanne H. , Hong Yeonsun , Kim Minsoo , Kam Lance C. , Salaita Khalid , Huse Morgan 
Published: June 2022

AbstractCytotoxic lymphocytes fight pathogens and cancer by forming immune synapses with infected or transformed target cells and then secreting cytotoxic perforin and granzyme into the synaptic space, with potent and specific killing achieved by this focused delivery. The mechanisms that establish the precise location of secretory events, however, remain poorly understood. Here we use single cell biophysical measurements, micropatterning, and functional assays to demonstrate that localized mechanotransduction helps define the position of secretory events within the synapse. Ligand-bound integrins, predominantly the αLβ2isoform LFA-1, function as spatial cues to attract lytic granules containing perforin and granzyme and induce their fusion with the plasma membrane for content release. LFA-1 is subjected to pulling forces within secretory domains, and disruption of these forces via depletion of the adaptor molecule talin abrogates cytotoxicity. We thus conclude that lymphocytes employ an integrin-dependent mechanical checkpoint to enhance their cytotoxic power and fidelity.
Microfluidics for understanding model organisms
Authors: Frey Nolan , Sönmez Utku M. , Minden Jonathan , LeDuc Philip 
Published: June 2022

AbstractNew microfluidic systems for whole organism analysis and experimentation are catalyzing biological breakthroughs across many fields, from human health to fundamental biology principles. This perspective discusses recent microfluidic tools to study intact model organisms to demonstrate the tremendous potential for these integrated approaches now and into the future. We describe these microsystems' technical features and highlight the unique advantages for precise manipulation in areas including immobilization, automated alignment, sorting, sensory, mechanical and chemical stimulation, and genetic and thermal perturbation. Our aim is to familiarize technologically focused researchers with microfluidics applications in biology research, while providing biologists an entrée to advanced microengineering techniques for model organisms.
Norepinephrine potentiates and serotonin depresses visual cortical responses by transforming eligibility traces
Authors: Hong Su Z. , Mesik Lukas , Grossman Cooper D. , Cohen Jeremiah Y. , Lee Boram , Severin Daniel , Lee Hey-Kyoung , Hell Johannes W. , Kirkwood Alfredo 
Published: June 2022

AbstractReinforcement allows organisms to learn which stimuli predict subsequent biological relevance. Hebbian mechanisms of synaptic plasticity are insufficient to account for reinforced learning because neuromodulators signaling biological relevance are delayed with respect to the neural activity associated with the stimulus. A theoretical solution is the concept of eligibility traces (eTraces), silent synaptic processes elicited by activity which upon arrival of a neuromodulator are converted into a lasting change in synaptic strength. Previously we demonstrated in visual cortical slices the Hebbian induction of eTraces and their conversion into LTP and LTD by the retroactive action of norepinephrine and serotonin Here we show in vivo in mouse V1 that the induction of eTraces and their conversion to LTP/D by norepinephrine and serotonin respectively potentiates and depresses visual responses. We also show that the integrity of this process is crucial for ocular dominance plasticity, a canonical model of experience-dependent plasticity.
Resilience of urban public electric vehicle charging infrastructure to flooding
Authors: Raman Gururaghav , Raman Gurupraanesh , Peng Jimmy Chih-Hsien 
Published: June 2022

AbstractAn adequate charging infrastructure is key to enabling high personal electric vehicle (EV) adoption rates. However, urban flooding—whose frequency and intensity are increasing due to climate change—may be an impediment. Here, we study how geographically-correlated outages due to floods impact public EV charging networks in Greater London. While we find no appreciable impact on the ability of battery EVs to serve typical urban driving behaviors, we observe disproportionate stresses on chargers both near, and surprisingly significantly farther from, the flooded regions. For instance, we find over 50% increase in charger utilization and 260% increase in the distance to the nearest available charger in parts of Greater London over 10 km away. Concerningly, the impact is most concentrated on already-stressed sections of the network, underscoring the infrastructure’s vulnerability. Finally, we develop and evaluate four strategies for city planners to enhance the flood resilience of cities’ public EV charging networks.
Structural Basis for pH-gating of the K+ channel TWIK1 at the selectivity filter
Authors: Turney Toby S. , Li Vivian , Brohawn Stephen G. 
Published: June 2022

AbstractTWIK1 (K2P1.1, KCNK1) is a widely expressed pH-gated two-pore domain K+ channel (K2P) that contributes to cardiac rhythm generation and insulin release from pancreatic beta cells. TWIK1 displays unique properties among K2Ps including low basal activity and inhibition by extracellular protons through incompletely understood mechanisms. Here, we present cryo-EM structures of TWIK1 in lipid nanodiscs at high and low pH that reveal a previously undescribed gating mechanism at the K+ selectivity filter. At high pH, TWIK1 adopts an open conformation. At low pH, protonation of an extracellular histidine results in a cascade of conformational changes that close the channel by sealing the top of the selectivity filter, displacing the helical cap to block extracellular ion access pathways, and opening gaps for lipid block of the intracellular cavity. These data provide a mechanistic understanding for extracellular pH-gating of TWIK1 and illustrate how diverse mechanisms have evolved to gate the selectivity filter of K+ channels.
Synthesis of a donor–acceptor heterodimer via trifunctional completive self-sorting
Authors: Kumar Sunit , Maurya Yogesh Kumar , Lis Tadeusz , Stępień Marcin 
Published: June 2022

AbstractSelective self-assembly of heterodimers consisting of two non-identical subunits plays important roles in Nature but is rarely encountered in synthetic supramolecular systems. Here we show that photocleavage of a donor–acceptor porphyrin complex produces an heterodimeric structure with surprising selectivity. The system forms via a multi-step sequence that starts with an oxidative ring opening, which produces an equimolar mixture of two isomeric degradation products (zinc(II) bilatrien-abc-ones, BTOs). These two isomers are susceptible to water addition, yielding the corresponding zinc(II) 15-hydroxybiladien-ab-ones (HBDOs). However, in the photocleavage experiment only one HBDO isomer is formed, and it quantitatively combines with the remaining BTO isomer. The resulting heterodimer is stabilized by a Zn–O coordination bond and extended dispersion interactions between the overlapping π-surfaces of the monomers. The observed selectivity can be seen as a case of completive self-sorting, simultaneously controlled by three types of complementary interactions.
Transformation of dolutegravir into an ultra-long-acting parenteral prodrug formulation
Authors: Deodhar Suyash , Sillman Brady , Bade Aditya N. , Avedissian Sean N. , Podany Anthony T. , McMillan JoEllyn M. , Gautam Nagsen , Hanson Brandon , Dyavar Shetty Bhagya L. , Szlachetka Adam , Johnston Morgan , Thurman Michellie , Munt Daniel J. , Dash Alekha K. , Markovic Milica , Dahan Arik , Alnouti Yazen , Yazdi Alborz , Kevadiya Bhavesh D. , Byrareddy Siddappa N. , Cohen Samuel M. , Edagwa Benson , Gendelman Howard E. 
Published: June 2022

AbstractUltra-long-acting integrase strand transfer inhibitors were created by screening a library of monomeric and dimeric dolutegravir (DTG) prodrug nanoformulations. This led to an 18-carbon chain modified ester prodrug nanocrystal (coined NM2DTG) with the potential to sustain yearly dosing. Here, we show that the physiochemical and pharmacokinetic (PK) formulation properties facilitate slow drug release from tissue macrophage depot stores at the muscle injection site and adjacent lymphoid tissues following single parenteral injection. Significant plasma drug levels are recorded up to a year following injection. Tissue sites for prodrug hydrolysis are dependent on nanocrystal dissolution and prodrug release, drug-depot volume, perfusion, and cell-tissue pH. Each affect an extended NM2DTG apparent half-life recorded by PK parameters. The NM2DTG product can impact therapeutic adherence, tolerability, and access of a widely used integrase inhibitor in both resource limited and rich settings to reduce HIV-1 transmission and achieve optimal treatment outcomes.
Robust and accurate estimation of paralog-specific copy number for duplicated genes using whole-genome sequencing
Authors: Prodanov Timofey , Bansal Vikas 
Published: June 2022

AbstractThe human genome contains hundreds of low-copy repeats (LCRs) that are challenging to analyze using short-read sequencing technologies due to extensive copy number variation and ambiguity in read mapping. Copy number and sequence variants in more than 150 duplicated genes that overlap LCRs have been implicated in monogenic and complex human diseases. We describe a computational tool, Parascopy, for estimating the aggregate and paralog-specific copy number of duplicated genes using whole-genome sequencing (WGS). Parascopy is an efficient method that jointly analyzes reads mapped to different repeat copies without the need for global realignment. It leverages multiple samples to mitigate sequencing bias and to identify reliable paralogous sequence variants (PSVs) that differentiate repeat copies. Analysis of WGS data for 2504 individuals from diverse populations showed that Parascopy is robust to sequencing bias, has higher accuracy compared to existing methods and enables prioritization of pathogenic copy number changes in duplicated genes.
Ultra-sensitive polarization-resolved black phosphorus homojunction photodetector defined by ferroelectric domains
Authors: Wu Shuaiqin , Chen Yan , Wang Xudong , Jiao Hanxue , Zhao Qianru , Huang Xinning , Tai Xiaochi , Zhou Yong , Chen Hao , Wang Xingjun , Huang Shenyang , Yan Hugen , Lin Tie , Shen Hong , Hu Weida , Meng Xiangjian , Chu Junhao , Wang Jianlu 
Published: June 2022

AbstractWith the further miniaturization and integration of multi-dimensional optical information detection devices, polarization-sensitive photodetectors based on anisotropic low-dimension materials have attractive potential applications. However, the performance of these devices is restricted by intrinsic property of materials leading to a small polarization ratio of the detectors. Here, we construct a black phosphorus (BP) homojunction photodetector defined by ferroelectric domains with ultra-sensitive polarization photoresponse. With the modulation of ferroelectric field, the BP exhibits anisotropic dispersion changes, leading an increased photothermalelectric (PTE) current in the armchair (AC) direction. Moreover, the PN junction can promote the PTE current and accelerate carrier separation. As a result, the BP photodetector demonstrates an ultrahigh polarization ratio (PR) of 288 at 1450 nm incident light, a large photoresponsivity of 1.06 A/W, and a high detectivity of 1.27 × 1011cmHz1/2W−1at room temperature. This work reveals the great potential of BP in future polarized light detection.
Optical control of exciton spin dynamics in layered metal halide perovskites via polaronic state formation
Authors: Bourelle Sean A. , Camargo Franco V. A. , Ghosh Soumen , Neumann Timo , van de Goor Tim W. J. , Shivanna Ravichandran , Winkler Thomas , Cerullo Giulio , Deschler Felix 
Published: June 2022

AbstractOne of the open challenges of spintronics is to control the spin relaxation mechanisms. Layered metal-halide perovskites are an emerging class of semiconductors which possess a soft crystal lattice that strongly couples electronic and vibrational states and show promise for spintronic applications. Here, we investigate the impact of such strong coupling on the spin relaxation of excitons in the layered perovskite BA2FAPbI7 using a combination of cryogenic Faraday rotation and transient absorption spectroscopy. We report an unexpected increase of the spin lifetime by two orders of magnitude at 77 K under photoexcitation with photon energy in excess of the exciton absorption peak, and thus demonstrate optical control over the dominant spin relaxation mechanism. We attribute this control to strong coupling between excitons and optically excited phonons, which form polaronic states with reduced electron-hole wave function overlap that protect the exciton spin memory. Our insights highlight the special role of exciton-lattice interactions on the spin physics in the layered perovskites and provide a novel opportunity for optical spin control.
Malaria oocysts require circumsporozoite protein to evade mosquito immunity
Authors: Zhu Feng , Zheng Hong , Chen Suilin , Zhang Kun , Qin Xin , Zhang Jingru , liu Taiping , Fan Yongling , Wang Liting , Li Xiaoxu , Zhang Jian , Xu Wenyue 
Published: June 2022

AbstractMalaria parasites are less vulnerable to mosquito immune responses once ookinetes transform into oocysts, facilitating parasite development in the mosquito. However, the underlying mechanisms of oocyst resistance to mosquito defenses remain unclear. Here, we show that circumsporozoite protein (CSP) is required for rodent malaria oocysts to avoid mosquito defenses. Mosquito infection with CSPmut parasites (mutation in the CSP pexel I/II domains) induces nicotinamide adenine dinucleotide phosphate (NADPH) oxidase 5 (NOX5)-mediated hemocyte nitration, thus activating Toll pathway and melanization of mature oocysts, upregulating hemocyte TEP1 expression, and causing defects in the release of sporozoites from oocysts. The pre-infection of mosquitoes with the CSPmut parasites reduces the burden of infection when re-challenged with CSPwt parasites by inducing hemocyte nitration. Thus, we demonstrate why oocysts are invisible to mosquito immunity and reveal an unknown role of CSP in the immune evasion of oocysts, indicating it as a potential target to block malaria transmission.
A single-cell transcriptomic atlas characterizes the silk-producing organ in the silkworm
Authors: Ma Yan , Zeng Wenhui , Ba Yongbing , Luo Qin , Ou Yao , Liu Rongpeng , Ma Jingwen , Tang Yiyun , Hu Jie , Wang Haomiao , Tang Xuan , Mu Yuanyuan , Li Qingjun , Chen Yuqin , Ran Yiting , Xiang Zhonghuai , Xu Hanfu 
Published: June 2022

AbstractThe silk gland of the domesticated silkworm Bombyx mori, is a remarkable organ that produces vast amounts of silk with exceptional properties. Little is known about which silk gland cells execute silk protein synthesis and its precise spatiotemporal control. Here, we use single-cell RNA sequencing to build a comprehensive cell atlas of the silkworm silk gland, consisting of 14,972 high-quality cells representing 10 distinct cell types, in three early developmental stages. We annotate all 10 cell types and determine their distributions in each region of the silk gland. Additionally, we decode the developmental trajectory and gene expression status of silk gland cells. Finally, we discover marker genes involved in the regulation of silk gland development and silk protein synthesis. Altogether, this work reveals the heterogeneity of silkworm silk gland cells and their gene expression dynamics, affording a deeper understanding of silk-producing organs at the single-cell level.
The role of references and the elusive nature of the chemical bond
Authors: Martín Pendás Ángel , Francisco Evelio 
Published: June 2022

AbstractChemical bonding theory is of utmost importance to chemistry, and a standard paradigm in which quantum mechanical interference drives the kinetic energy lowering of two approaching fragments has emerged. Here we report that both internal and external reference biases remain in this model, leaving plenty of unexplored territory. We show how the former biases affect the notion of wavefunction interference, which is purportedly recognized as the most basic bonding mechanism. The latter influence how bonding models are chosen. We demonstrate that the use of real space analyses are as reference-less as possible, advocating for their use. Delocalisation emerges as the reference-less equivalent to interference and the ultimate root of bonding. Atoms (or fragments) in molecules should be understood as a statistical mixture of components differing in electron number, spin, etc.