bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell spatial metabolomics with cell-type specific protein profiling for tissue systems biology
Authors: Hu Thomas , Allam Mayar , Cai Shuangyi , Henderson Walter , Yueh Brian , Garipcan Aybuke , Ievlev Anton V. , Afkarian Maryam , Beyaz Semir , Coskun Ahmet F. 
Published: December 2023

AbstractMetabolic reprogramming in cancer and immune cells occurs to support their increasing energy needs in biological tissues. Here we propose Single Cell Spatially resolved Metabolic (scSpaMet) framework for joint protein-metabolite profiling of single immune and cancer cells in male human tissues by incorporating untargeted spatial metabolomics and targeted multiplexed protein imaging in a single pipeline. We utilized the scSpaMet to profile cell types and spatial metabolomic maps of 19507, 31156, and 8215 single cells in human lung cancer, tonsil, and endometrium tissues, respectively. The scSpaMet analysis revealed cell type-dependent metabolite profiles and local metabolite competition of neighboring single cells in human tissues. Deep learning-based joint embedding revealed unique metabolite states within cell types. Trajectory inference showed metabolic patterns along cell differentiation paths. Here we show scSpaMet’s ability to quantify and visualize the cell-type specific and spatially resolved metabolic-protein mapping as an emerging tool for systems-level understanding of tissue biology.
Embedding security into ferroelectric FET array via in situ memory operation
Authors: Xu Yixin , Xiao Yi , Zhao Zijian , Müller Franz , Vardar Alptekin , Gong Xiao , George Sumitha , Kämpfe Thomas , Narayanan Vijaykrishnan , Ni Kai 
Published: December 2023

AbstractNon-volatile memories (NVMs) have the potential to reshape next-generation memory systems because of their promising properties of near-zero leakage power consumption, high density and non-volatility. However, NVMs also face critical security threats that exploit the non-volatile property. Compared to volatile memory, the capability of retaining data even after power down makes NVM more vulnerable. Existing solutions to address the security issues of NVMs are mainly based on Advanced Encryption Standard (AES), which incurs significant performance and power overhead. In this paper, we propose a lightweight memory encryption/decryption scheme by exploiting in-situ memory operations with negligible overhead. To validate the feasibility of the encryption/decryption scheme, device-level and array-level experiments are performed using ferroelectric field effect transistor (FeFET) as an example NVM without loss of generality. Besides, a comprehensive evaluation is performed on a 128 × 128 FeFET AND-type memory array in terms of area, latency, power and throughput. Compared with the AES-based scheme, our scheme shows ~22.6×/~14.1× increase in encryption/decryption throughput with negligible power penalty. Furthermore, we evaluate the performance of our scheme over the AES-based scheme when deploying different neural network workloads. Our scheme yields significant latency reduction by 90% on average for encryption and decryption processes.
Remote transport of high-dimensional orbital angular momentum states and ghost images via spatial-mode-engineered frequency conversion
Authors: Qiu Xiaodong , Guo Haoxu , Chen Lixiang 
Published: December 2023

AbstractThe efficient transport and engineering of photonic orbital angular momentum (OAM) lie at the heart of various related classical and quantum applications. Here, by leveraging the spatial-mode-engineered frequency conversion, we realize the remote transport of high-dimensional orbital angular momentum (OAM) states between two distant parties without direct transmission of information carriers. We exploit perfect vortices for preparing high-dimensional yet maximal O AM entanglement. Based on nonlinear sum-frequency generation working with a strong coherent wave packet and a single photon, we conduct the Bell-like state measurements for high-dimensional perfect vortices. We experimentally achieve an average transport fidelity 0.879 ± 0.048 and 0.796 ± 0.066 for a complete set of 3-dimensional and 5-dimensional OAM mutually unbiased bases, respectively. Furthermore, by exploring the full transverse entanglement, we construct another strategy of quantum imaging with interaction-free light. It is expected that, with the future advances in nonlinear frequency conversion, our scheme will pave the way for realizing truly secure high-dimensional quantum teleportation in the upcoming quantum network.
A coherent phonon-induced hidden quadrupolar ordered state in Ca2RuO4
Authors: Ning Honglie , Mehio Omar , Li Xinwei , Buchhold Michael , Driesse Mathias , Zhao Hengdi , Cao Gang , Hsieh David 
Published: December 2023

AbstractUltrafast laser excitation provides a means to transiently realize long-range ordered electronic states of matter that are hidden in thermal equilibrium. Recently, this approach has unveiled a variety of thermally inaccessible ordered states in strongly correlated materials, including charge density wave, ferroelectric, magnetic, and intertwined charge-orbital ordered states. However, more exotic hidden states exhibiting higher multipolar ordering remain elusive owing to the challenge of directly manipulating and detecting them with light. Here we demonstrate a method to induce a dynamical transition from a thermally allowed to a thermally forbidden spin-orbit entangled quadrupolar ordered state in Ca2RuO4 by coherently exciting a phonon that is strongly coupled to the order parameter. Combining probe photon energy-resolved coherent phonon spectroscopy measurements with model Hamiltonian calculations, we show that the dynamical transition is manifested through anomalies in the temperature, pump excitation fluence, and probe photon energy dependence of the strongly coupled phonon. With this procedure, we introduce a general pathway to uncover hidden multipolar ordered states and to control their re-orientation on ultrashort timescales.
Phase-dependent Andreev molecules and superconducting gap closing in coherently-coupled Josephson junctions
Authors: Matsuo Sadashige , Imoto Takaya , Yokoyama Tomohiro , Sato Yosuke , Lindemann Tyler , Gronin Sergei , Gardner Geoffrey C. , Nakosai Sho , Tanaka Yukio , Manfra Michael J. , Tarucha Seigo 
Published: December 2023

AbstractThe Josephson junction (JJ) is an essential element of superconducting (SC) devices for both fundamental and applied physics. The short-range coherent coupling of two adjacent JJs forms Andreev molecule states (AMSs), which provide a new ingredient to engineer exotic SC phenomena such as topological SC states and Andreev qubits. Here we provide tunneling spectroscopy measurements on a device consisting of two electrically controllable planar JJs sharing a single SC electrode. We discover that Andreev spectra in the coupled JJ are highly modulated from those in the single JJs and possess phase-dependent AMS features reproduced in our numerical calculation. Notably, the SC gap closing due to the AMS formation is experimentally observed. Our results help in understanding SC transport derived from the AMS and promoting the use of AMS physics to engineer topological SC states and quantum information devices.
Uncertainties in deforestation emission baseline methodologies and implications for carbon markets
Authors: Teo Hoong Chen , Tan Nicole Hui Li , Zheng Qiming , Lim Annabel Jia Yi , Sreekar Rachakonda , Chen Xiao , Zhou Yuchuan , Sarira Tasya Vadya , De Alban Jose Don T. , Tang Hao , Friess Daniel A. , Koh Lian Pin 
Published: December 2023

AbstractCarbon credits generated through jurisdictional-scale avoided deforestation projects require accurate estimates of deforestation emission baselines, but there are serious challenges to their robustness. We assessed the variability, accuracy, and uncertainty of baselining methods by applying sensitivity and variable importance analysis on a range of typically-used methods and parameters for 2,794 jurisdictions worldwide. The median jurisdiction’s deforestation emission baseline varied by 171% (90% range: 87%-440%) of its mean, with a median forecast error of 0.778 times (90% range: 0.548-3.56) the actual deforestation rate. Moreover, variable importance analysis emphasised the strong influence of the deforestation projection approach. For the median jurisdiction, 68.0% of possible methods (90% range: 61.1%-85.6%) exceeded 15% uncertainty. Tropical and polar biomes exhibited larger uncertainties in carbon estimations. The use of sensitivity analyses, multi-model, and multi-source ensemble approaches could reduce variabilities and biases. These findings provide a roadmap for improving baseline estimations to enhance carbon market integrity and trust.
A corrosion inhibiting layer to tackle the irreversible lithium loss in lithium metal batteries
Authors: Jin Chengbin , Huang Yiyu , Li Lanhang , Wei Guoying , Li Hongyan , Shang Qiyao , Ju Zhijin , Lu Gongxun , Zheng Jiale , Sheng Ouwei , Tao Xinyong 
Published: December 2023

AbstractReactive negative electrodes like lithium (Li) suffer serious chemical and electrochemical corrosion by electrolytes during battery storage and operation, resulting in rapidly deteriorated cyclability and short lifespans of batteries. Li corrosion supposedly relates to the features of solid-electrolyte-interphase (SEI). Herein, we quantitatively monitor the Li corrosion and SEI progression (e.g., dissolution, reformation) in typical electrolytes through devised electrochemical tools and cryo-electron microscopy. The continuous Li corrosion is validated to be positively correlated with SEI dissolution. More importantly, an anti-corrosion and interface-stabilizing artificial passivation layer comprising low-solubility polymer and metal fluoride is designed. Prolonged operations of Li symmetric cells and Li | |LiFePO4 cells with reduced Li corrosion by ~74% are achieved (0.66 versus 2.5 μAh h−1). The success can further be extended to ampere-hour-scale pouch cells. This work uncovers the SEI dissolution and its correlation with Li corrosion, enabling the durable operation of Li metal batteries by reducing the Li loss.
A physics informed bayesian optimization approach for material design: application to NiTi shape memory alloys
Authors: Khatamsaz Danial , Neuberger Raymond , Roy Arunabha M. , Zadeh Sina Hossein , Otis Richard , Arróyave Raymundo 
Published: December 2023

AbstractThe design of materials and identification of optimal processing parameters constitute a complex and challenging task, necessitating efficient utilization of available data. Bayesian Optimization (BO) has gained popularity in materials design due to its ability to work with minimal data. However, many BO-based frameworks predominantly rely on statistical information, in the form of input-output data, and assume black-box objective functions. In practice, designers often possess knowledge of the underlying physical laws governing a material system, rendering the objective function not entirely black-box, as some information is partially observable. In this study, we propose a physics-informed BO approach that integrates physics-infused kernels to effectively leverage both statistical and physical information in the decision-making process. We demonstrate that this method significantly improves decision-making efficiency and enables more data-efficient BO. The applicability of this approach is showcased through the design of NiTi shape memory alloys, where the optimal processing parameters are identified to maximize the transformation temperature.
Spread in climate policy scenarios unravelled
Authors: Dekker Mark M. , Hof Andries F. , van den Berg Maarten , Daioglou Vassilis , van Heerden Rik , van der Wijst Kaj-Ivar , van Vuuren Detlef P. 
Published: December 2023

AbstractAnalysis of climate policy scenarios has become an important tool for identifying mitigation strategies, as shown in the latest Intergovernmental Panel on Climate Change Working Group III report1. The key outcomes of these scenarios differ substantially not only because of model and climate target differences but also because of different assumptions on behavioural, technological and socio-economic developments2–4. A comprehensive attribution of the spread in climate policy scenarios helps policymakers, stakeholders and scientists to cope with large uncertainties in this field. Here we attribute this spread to the underlying drivers using Sobol decomposition5, yielding the importance of each driver for scenario outcomes. As expected, the climate target explains most of the spread in greenhouse gas emissions, total and sectoral fossil fuel use, total renewable energy and total carbon capture and storage in electricity generation. Unexpectedly, model differences drive variation of most other scenario outcomes, for example, in individual renewable and carbon capture and storage technologies, and energy in demand sectors, reflecting intrinsic uncertainties about long-term developments and the range of possible mitigation strategies. Only a few scenario outcomes, such as hydrogen use, are driven by other scenario assumptions, reflecting the need for more scenario differentiation. This attribution analysis distinguishes areas of consensus as well as strong model dependency, providing a crucial step in correctly interpreting scenario results for robust decision-making.
A transcriptomic taxonomy of mouse brain-wide spinal projecting neurons
Authors: Winter Carla C. , Jacobi Anne , Su Junfeng , Chung Leeyup , van Velthoven Cindy T. J. , Yao Zizhen , Lee Changkyu , Zhang Zicong , Yu Shuguang , Gao Kun , Duque Salazar Geraldine , Kegeles Evgenii , Zhang Yu , Tomihiro Makenzie C. , Zhang Yiming , Yang Zhiyun , Zhu Junjie , Tang Jing , Song Xuan , Donahue Ryan J. , Wang Qing , McMillen Delissa , Kunst Michael , Wang Ning , Smith Kimberly A. , Romero Gabriel E. , Frank Michelle M. , Krol Alexandra , Kawaguchi Riki , Geschwind Daniel H. , Feng Guoping , Goodrich Lisa V. , Liu Yuanyuan , Tasic Bosiljka , Zeng Hongkui , He Zhigang 
Published: December 2023

AbstractThe brain controls nearly all bodily functions via spinal projecting neurons (SPNs) that carry command signals from the brain to the spinal cord. However, a comprehensive molecular characterization of brain-wide SPNs is still lacking. Here we transcriptionally profiled a total of 65,002 SPNs, identified 76 region-specific SPN types, and mapped these types into a companion atlas of the whole mouse brain1. This taxonomy reveals a three-component organization of SPNs: (1) molecularly homogeneous excitatory SPNs from the cortex, red nucleus and cerebellum with somatotopic spinal terminations suitable for point-to-point communication; (2) heterogeneous populations in the reticular formation with broad spinal termination patterns, suitable for relaying commands related to the activities of the entire spinal cord; and (3) modulatory neurons expressing slow-acting neurotransmitters and/or neuropeptides in the hypothalamus, midbrain and reticular formation for ‘gain setting’ of brain–spinal signals. In addition, this atlas revealed a LIM homeobox transcription factor code that parcellates the reticulospinal neurons into five molecularly distinct and spatially segregated populations. Finally, we found transcriptional signatures of a subset of SPNs with large soma size and correlated these with fast-firing electrophysiological properties. Together, this study establishes a comprehensive taxonomy of brain-wide SPNs and provides insight into the functional organization of SPNs in mediating brain control of bodily functions.
Single-cell analysis of chromatin accessibility in the adult mouse brain
Authors: Zu Songpeng , Li Yang Eric , Wang Kangli , Armand Ethan J. , Mamde Sainath , Amaral Maria Luisa , Wang Yuelai , Chu Andre , Xie Yang , Miller Michael , Xu Jie , Wang Zhaoning , Zhang Kai , Jia Bojing , Hou Xiaomeng , Lin Lin , Yang Qian , Lee Seoyeon , Li Bin , Kuan Samantha , Liu Hanqing , Zhou Jingtian , Pinto-Duarte Antonio , Lucero Jacinta , Osteen Julia , Nunn Michael , Smith Kimberly A. , Tasic Bosiljka , Yao Zizhen , Zeng Hongkui , Wang Zihan , Shang Jingbo , Behrens M. Margarita , Ecker Joseph R. , Wang Allen , Preissl Sebastian , Ren Bing 
Published: December 2023

AbstractRecent advances in single-cell technologies have led to the discovery of thousands of brain cell types; however, our understanding of the gene regulatory programs in these cell types is far from complete1–4. Here we report a comprehensive atlas of candidate cis-regulatory DNA elements (cCREs) in the adult mouse brain, generated by analysing chromatin accessibility in 2.3 million individual brain cells from 117 anatomical dissections. The atlas includes approximately 1 million cCREs and their chromatin accessibility across 1,482 distinct brain cell populations, adding over 446,000 cCREs to the most recent such annotation in the mouse genome. The mouse brain cCREs are moderately conserved in the human brain. The mouse-specific cCREs—specifically, those identified from a subset of cortical excitatory neurons—are strongly enriched for transposable elements, suggesting a potential role for transposable elements in the emergence of new regulatory programs and neuronal diversity. Finally, we infer the gene regulatory networks in over 260 subclasses of mouse brain cells and develop deep-learning models to predict the activities of gene regulatory elements in different brain cell types from the DNA sequence alone. Our results provide a resource for the analysis of cell-type-specific gene regulation programs in both mouse and human brains.
Biophosphorescence in fluorescent millipedes (Diplopoda: Xystodesmidae) and its relationships with bioluminescence
Authors: Viviani Vadim R. 
Published: December 2023

AbstractThree types of luminescence have been reported in living organisms: bioluminescence (BL), ultraweak chemiluminescence and biofluorescence (FL). In millipedes, both BL and FL have been reported in Motyxia sequoiae and related Xystodesmidae species. Noteworthy, when walking at night with a UV lantern at the Biological Station of Highlands, I found three blue-fluorescent millipedes (Deltotaria brimleii, Deltotoria sp and Euryus orestes) that also displayed phosphorescence after turning off the UV source. The phosphorescence of the cuticle was in the green region (λmax = 525 nm). The phosphorescence remained associated with cuticle and pellets, but frozen fluorescent supernatants, also displayed phosphorescence. The fluorescent compounds extracted from the cuticles in water and methanol and separated by TLC, displayed fluorescence spectra similar to that of 6-pteridine carboxylic acid. In contrast to Motyxia sequoiae cuticle extracts, no bioluminescence was found in Deltatoria and Euryus extracts in the presence of MgATP, but weak green chemiluminescence was detected with H2O2 and superoxide. The spectral overlapping of phosphorescence of these millipedes with the bioluminescence of Motyxia (~ 507 nm) and the intimate association of both types of luminescence with the cuticles, raises the possibility that bioluminescence in Motyxia may arise from chemiluminescence reactions preferentially generating triplet excited states instead of singlet states.
An inventory of human light exposure behaviour
Authors: Siraji Mushfiqul Anwar , Lazar Rafael Robert , van Duijnhoven Juliëtte , Schlangen Luc J. M. , Haque Shamsul , Kalavally Vineetha , Vetter Céline , Glickman Gena L. , Smolders Karin C. H. J. , Spitschan Manuel 
Published: December 2023

AbstractLight exposure is an essential driver of health and well-being, and individual behaviours during rest and activity modulate physiologically relevant aspects of light exposure. Further understanding the behaviours that influence individual photic exposure patterns may provide insight into the volitional contributions to the physiological effects of light and guide behavioural points of intervention. Here, we present a novel, self-reported and psychometrically validated inventory to capture light exposure-related behaviour, the Light Exposure Behaviour Assessment (LEBA). An expert panel prepared the initial 48-item pool spanning different light exposure-related behaviours. Responses, consisting of rating the frequency of engaging in the per-item behaviour on a five-point Likert-type scale, were collected in an online survey yielding responses from a geographically unconstrained sample (690 completed responses, 74 countries, 28 time zones). The exploratory factor analysis (EFA) on an initial subsample (n = 428) rendered a five-factor solution with 25 items (wearing blue light filters, spending time outdoors, using a phone and smartwatch in bed, using light before bedtime, using light in the morning and during daytime). In a confirmatory factor analysis (CFA) performed on an independent subset of participants (n = 262), we removed two additional items to attain the best fit for the five-factor solution (CFI = 0.95, TLI = 0.95, RMSEA = 0.06). The internal consistency reliability coefficient for the total instrument yielded McDonald’s Omega = 0.68. Measurement model invariance analysis between native and non-native English speakers showed our model attained the highest level of invariance (residual invariance CFI = 0.95, TLI = 0.95, RMSEA = 0.05). Lastly, a short form of the LEBA (n = 18 items) was developed using Item Response Theory on the complete sample (n = 690). The psychometric properties of the LEBA indicate the usability for measuring light exposure-related behaviours. The instrument may offer a scalable solution to characterise behaviours that influence individual photic exposure patterns in remote samples. The LEBA inventory is available under the open-access CC-BY license. Instrument webpage:https://leba-instrument.org/GitHub repository containing this manuscript:https://github.com/leba-instrument/leba-manuscript.
Accurate characterization of complex Bloch modes in optical chain waveguides using real-valued computations
Authors: Ghahremani Maryam , Shahabadi Mahmoud 
Published: December 2023

AbstractThis research presents a highly accurate and easy-to-implement method to characterize the complex Bloch modes propagating along optical chain waveguides with three-dimensional (3D) layered geometries and dispersive negative-epsilon material compositions. The technique combines commercial EM solver results with analytical post-processing to avoid iterative complex root estimation on the complex plane. The proposed methodology is based on the real-valued computations that yield the complex Bloch wavevector with superior accuracy even when both radiation and material losses are present. In addition, we introduce a single unit-cell technique to provide the possibility of dense meshing of 3D geometries when available computational resources are limited. To verify our results, two different plasmonic and dielectric case studies are discussed. The obtained results agree well with numerical and experimental results from the literature. Due to its generality, robustness, and high accuracy, the method is beneficial for studying a large variety of waveguide-based nanophotonic components.