bluuebunny/crossref_metadata_2025_split huggingface dataset:
Artificial light at night is a top predictor of bird migration stopover density
Authors: Horton Kyle G. , Buler Jeffrey J. , Anderson Sharolyn J. , Burt Carolyn S. , Collins Amy C. , Dokter Adriaan M. , Guo Fengyi , Sheldon Daniel , Tomaszewska Monika Anna , Henebry Geoffrey M. 
Published: December 2023

AbstractAs billions of nocturnal avian migrants traverse North America, twice a year they must contend with landscape changes driven by natural and anthropogenic forces, including the rapid growth of the artificial glow of the night sky. While airspaces facilitate migrant passage, terrestrial landscapes serve as essential areas to restore energy reserves and often act as refugia—making it critical to holistically identify stopover locations and understand drivers of use. Here, we leverage over 10 million remote sensing observations to develop seasonal contiguous United States layers of bird migrant stopover density. In over 70% of our models, we identify skyglow as a highly influential and consistently positive predictor of bird migration stopover density across the United States. This finding points to the potential of an expanding threat to avian migrants: peri-urban illuminated areas may act as ecological traps at macroscales that increase the mortality of birds during migration.
Transmembrane coupling of liquid-like protein condensates
Authors: Lee Yohan , Park Sujin , Yuan Feng , Hayden Carl C. , Wang Liping , Lafer Eileen M. , Choi Siyoung Q. , Stachowiak Jeanne C. 
Published: December 2023

AbstractLiquid-liquid phase separation of proteins occurs on both surfaces of cellular membranes during diverse physiological processes. In vitro reconstitution could provide insight into the mechanisms underlying these events. However, most existing reconstitution techniques provide access to only one membrane surface, making it difficult to probe transmembrane phenomena. To study protein phase separation simultaneously on both membrane surfaces, we developed an array of freestanding planar lipid membranes. Interestingly, we observed that liquid-like protein condensates on one side of the membrane colocalized with those on the other side, resulting in transmembrane coupling. Our results, based on lipid probe partitioning and mobility of lipids, suggest that protein condensates locally reorganize membrane lipids, a process which could be explained by multiple effects. These findings suggest a mechanism by which signals originating on one side of a biological membrane, triggered by protein phase separation, can be transferred to the opposite side.
Gravitationally induced decoherence vs space-time diffusion: testing the quantum nature of gravity
Authors: Oppenheim Jonathan , Sparaciari Carlo , Šoda Barbara , Weller-Davies Zachary 
Published: December 2023

AbstractWe consider two interacting systems when one is treated classically while the other system remains quantum. Consistent dynamics of this coupling has been shown to exist, and explored in the context of treating space-time classically. Here, we prove that any such hybrid dynamics necessarily results in decoherence of the quantum system, and a breakdown in predictability in the classical phase space. We further prove that a trade-off between the rate of this decoherence and the degree of diffusion induced in the classical system is a general feature of all classical quantum dynamics; long coherence times require strong diffusion in phase-space relative to the strength of the coupling. Applying the trade-off relation to gravity, we find a relationship between the strength of gravitationally-induced decoherence versus diffusion of the metric and its conjugate momenta. This provides an experimental signature of theories in which gravity is fundamentally classical. Bounds on decoherence rates arising from current interferometry experiments, combined with precision measurements of mass, place significant restrictions on theories where Einstein’s classical theory of gravity interacts with quantum matter. We find that part of the parameter space of such theories are already squeezed out, and provide figures of merit which can be used in future mass measurements and interference experiments.
Dichotomy of heavy and light pairs of holes in the t−J model
Authors: Bohrdt A. , Demler E. , Grusdt F. 
Published: December 2023

AbstractA key step in unraveling the mysteries of materials exhibiting unconventional superconductivity is to understand the underlying pairing mechanism. While it is widely agreed upon that the pairing glue in many of these systems originates from antiferromagnetic spin correlations, a microscopic description of pairs of charge carriers remains lacking. Here we use state-of-the art numerical methods to probe the internal structure and dynamical properties of pairs of charge carriers in quantum antiferromagnets in four-legged cylinders. Exploiting the full momentum resolution in our simulations, we are able to distinguish two qualitatively different types of bound states: a highly mobile, meta-stable pair, which has a dispersion proportional to the hole hopping t, and a heavy pair, which can only move due to spin exchange processes and turns into a flat band in the Ising limit of the model. Understanding the pairing mechanism can on the one hand pave the way to boosting binding energies in related models, and on the other hand enable insights into the intricate competition of various phases of matter in strongly correlated electron systems.
A biotin targeting chimera (BioTAC) system to map small molecule interactomes in situ
Authors: Tao Andrew J. , Jiang Jiewei , Gadbois Gillian E. , Goyal Pavitra , Boyle Bridget T. , Mumby Elizabeth J. , Myers Samuel A. , English Justin G. , Ferguson Fleur M. 
Published: December 2023

AbstractUnderstanding how small molecules bind to specific protein complexes in living cells is critical to understanding their mechanism-of-action. Unbiased chemical biology strategies for direct readout of protein interactome remodelling by small molecules would provide advantages over target-focused approaches, including the ability to detect previously unknown ligand targets and complexes. However, there are few current methods for unbiased profiling of small molecule interactomes. To address this, we envisioned a technology that would combine the sensitivity and live-cell compatibility of proximity labelling coupled to mass spectrometry, with the specificity and unbiased nature of chemoproteomics. In this manuscript, we describe the BioTAC system, a small-molecule guided proximity labelling platform that can rapidly identify both direct and complexed small molecule binding proteins. We benchmark the system against µMap, photoaffinity labelling, affinity purification coupled to mass spectrometry and proximity labelling coupled to mass spectrometry datasets. We also apply the BioTAC system to provide interactome maps of Trametinib and analogues. The BioTAC system overcomes a limitation of current approaches and supports identification of both inhibitor bound and molecular glue bound complexes.
Spatiotemporal dynamics of traffic bottlenecks yields an early signal of heavy congestions
Authors: Duan Jinxiao , Zeng Guanwen , Serok Nimrod , Li Daqing , Lieberthal Efrat Blumenfeld , Huang Hai-Jun , Havlin Shlomo 
Published: December 2023

AbstractHeavy traffic jams are difficult to predict due to the complexity of traffic dynamics. Understanding the network dynamics of traffic bottlenecks can help avoid critical large traffic jams and improve overall traffic conditions. Here, we develop a method to forecast heavy congestions based on their early propagation stage. Our framework follows the network propagation and dissipation of the traffic jams originated from a bottleneck emergence, growth, and its recovery and disappearance. Based on large-scale urban traffic-speed data, we find that dissipation duration of jams follows approximately power-law distributions, and typically, traffic jams dissolve nearly twice slower than their growth. Importantly, we find that the growth speed, even at the first 15 minutes of a jam, is highly correlated with the maximal size of the jam. Our methodology can be applied in urban traffic control systems to forecast heavy traffic bottlenecks and prevent them before they propagate to large network congestions.
Unveiling patterns in human dominated landscapes through mapping the mass of US built structures
Authors: Frantz David , Schug Franz , Wiedenhofer Dominik , Baumgart André , Virág Doris , Cooper Sam , Gómez-Medina Camila , Lehmann Fabian , Udelhoven Thomas , van der Linden Sebastian , Hostert Patrick , Haberl Helmut 
Published: December 2023

AbstractBuilt structures increasingly dominate the Earth’s landscapes; their surging mass is currently overtaking global biomass. We here assess built structures in the conterminous US by quantifying the mass of 14 stock-building materials in eight building types and nine types of mobility infrastructures. Our high-resolution maps reveal that built structures have become 2.6 times heavier than all plant biomass across the country and that most inhabited areas are mass-dominated by buildings or infrastructure. We analyze determinants of the material intensity and show that densely built settlements have substantially lower per-capita material stocks, while highest intensities are found in sparsely populated regions due to ubiquitous infrastructures. Out-migration aggravates already high intensities in rural areas as people leave while built structures remain – highlighting that quantifying the distribution of built-up mass at high resolution is an essential contribution to understanding the biophysical basis of societies, and to inform strategies to design more resource-efficient settlements and a sustainable circular economy.
Photosensitizer-free visible-light-promoted glycosylation enabled by 2-glycosyloxy tropone donors
Authors: Zhang Jing , Luo Zhao-Xiang , Wu Xia , Gao Chen-Fei , Wang Peng-Yu , Chai Jin-Ze , Liu Miao , Ye Xin-Shan , Xiong De-Cai 
Published: December 2023

AbstractPhotochemical glycosylation has attracted considerable attention in carbohydrate chemistry. However, to the best of our knowledge, visible-light-promoted glycosylation via photoactive glycosyl donor has not been reported. In the study, we report a photosensitizer-free visible-light-mediated glycosylation approach using a photoactive 2-glycosyloxy tropone as the donor. This glycosylation reaction proceeds at ambient temperature to give a wide range of O-glycosides or oligosaccharides with yields up to 99%. This method is further applied in the stereoselective preparation of various functional glycosyl phosphates/phosphosaccharides, the construction of N-glycosides/nucleosides, and the late-stage glycosylation of natural products or pharmaceuticals on gram scales, and the iterative synthesis of hexasaccharide. The protocol features uncomplicated conditions, operational simplicity, wide substrate scope (58 examples), excellent compatibility with functional groups, scalability of products (7 examples), and high yields. It provides an efficient glycosylation method for accessing O/N-glycosides and glycans.
Combinatorial single-cell profiling of major chromatin types with MAbID
Authors: Lochs Silke J. A. , van der Weide Robin H. , de Luca Kim L. , Korthout Tessy , van Beek Ramada E. , Kimura Hiroshi , Kind Jop 
Published: December 2023

AbstractGene expression programs result from the collective activity of numerous regulatory factors. Studying their cooperative mode of action is imperative to understand gene regulation, but simultaneously measuring these factors within one sample has been challenging. Here we introduce Multiplexing Antibodies by barcode Identification (MAbID), a method for combinatorial genomic profiling of histone modifications and chromatin-binding proteins. MAbID employs antibody–DNA conjugates to integrate barcodes at the genomic location of the epitope, enabling combined incubation of multiple antibodies to reveal the distributions of many epigenetic markers simultaneously. We used MAbID to profile major chromatin types and multiplexed measurements without loss of individual data quality. Moreover, we obtained joint measurements of six epitopes in single cells of mouse bone marrow and during mouse in vitro differentiation, capturing associated changes in multifactorial chromatin states. Thus, MAbID holds the potential to gain unique insights into the interplay between gene regulatory mechanisms, especially for low-input samples and in single cells.
Uniform quantification of single-nucleus ATAC-seq data with Paired-Insertion Counting (PIC) and a model-based insertion rate estimator
Authors: Miao Zhen , Kim Junhyong 
Published: December 2023

AbstractExisting approaches to scoring single-nucleus assay for transposase-accessible chromatin with sequencing (snATAC-seq) feature matrices from sequencing reads are inconsistent, affecting downstream analyses and displaying artifacts. We show that, even with sparse single-cell data, quantitative counts are informative for estimating the regulatory state of a cell, which calls for a consistent treatment. We propose Paired-Insertion Counting as a uniform method for snATAC-seq feature characterization and provide a probability model for inferring latent insertion dynamics from snATAC-seq count matrices.
Rational optimization of a transcription factor activation domain inhibitor
Authors: Basu Shaon , Martínez-Cristóbal Paula , Frigolé-Vivas Marta , Pesarrodona Mireia , Lewis Michael , Szulc Elzbieta , Bañuelos C. Adriana , Sánchez-Zarzalejo Carolina , Bielskutė Stasė , Zhu Jiaqi , Pombo-García Karina , Garcia-Cabau Carla , Zodi Levente , Dockx Hannes , Smak Jordann , Kaur Harpreet , Batlle Cristina , Mateos Borja , Biesaga Mateusz , Escobedo Albert , Bardia Lídia , Verdaguer Xavier , Ruffoni Alessandro , Mawji Nasrin R. , Wang Jun , Obst Jon K. , Tam Teresa , Brun-Heath Isabelle , Ventura Salvador , Meierhofer David , García Jesús , Robustelli Paul , Stracker Travis H. , Sadar Marianne D. , Riera Antoni , Hnisz Denes , Salvatella Xavier 
Published: December 2023

AbstractTranscription factors are among the most attractive therapeutic targets but are considered largely ‘undruggable’ in part due to the intrinsically disordered nature of their activation domains. Here we show that the aromatic character of the activation domain of the androgen receptor, a therapeutic target for castration-resistant prostate cancer, is key for its activity as transcription factor, allowing it to translocate to the nucleus and partition into transcriptional condensates upon activation by androgens. On the basis of our understanding of the interactions stabilizing such condensates and of the structure that the domain adopts upon condensation, we optimized the structure of a small-molecule inhibitor previously identified by phenotypic screening. The optimized compounds had more affinity for their target, inhibited androgen-receptor-dependent transcriptional programs, and had an antitumorigenic effect in models of castration-resistant prostate cancer in cells and in vivo. These results suggest that it is possible to rationally optimize, and potentially even to design, small molecules that target the activation domains of oncogenic transcription factors.
Signature methods for brain-computer interfaces
Authors: Xu Xiaoqi , Lee Darrick , Drougard Nicolas , Roy Raphaëlle N. 
Published: December 2023

AbstractBrain-computer interfaces (BCIs) allow direct communication between one’s central nervous system and a computer without any muscle movement hence by-passing the peripheral nervous system. They can restore disabled people’s ability to interact with their environment, e.g. communication and wheelchair control. However, to this day their performance is still hindered by the non-stationarity of electroencephalography (EEG) signals, as well as their susceptibility to noise from the users’ environment and from their own physiological activity. Moreover, a non-negligible amount of users struggle to use BCI systems based on motor imagery. In this paper, a new method based on the path signature is introduced to tackle this problem by using features which are different from the usual power-based ones. The path signature is a series of iterated integrals computed from a multidimensional path. It is invariant under translation and time reparametrization, which makes it a robust feature for multichannel EEG time series. The performance can be further boosted by combining the path signature with the gold standard Riemannian classifier in the BCI field exploiting the geometric structure of symmetric positive definite (SPD) matrices. The results obtained on publicly available datasets show that the signature method is more robust to inter-user variability than classical ones, especially on noisy and low-quality data. Hence, this study paves the way towards the use of mathematical tools that until now have been neglected, in order to tackle the EEG-based BCI variability issue. It also sheds light on the lead-lag relationship captured by path signature which seems relevant to assess the underlying neural mechanisms.
SSD with multi-scale feature fusion and attention mechanism
Authors: Liu Qiang , Dong Lijun , Zeng Zhigao , Zhu Wenqiu , Zhu Yanhui , Meng Chen 
Published: December 2023

AbstractIn the field of the Internet of Things, image acquisition equipment is the very important equipment, which will generate lots of invalid data during real-time monitoring. Analyzing the data collected directly from the terminal by edge calculation, we can remove invalid frames and improve the accuracy of system detection. SSD algorithm has a relatively light and fast detection speed. However, SSD algorithm do not take full advantage of both shallow and deep information of data. So a multiscale feature fusion attention mechanism structure based on SSD algorithm has been proposed in this paper, which combines multiscale feature fusion and attention mechanism. The adjacent feature layers for each detection layer are fused to improve the feature information expression ability. Then, the attention mechanism is added to increase the attention of the feature map channels. The results of the experiments show that the detection accuracy of the optimized model is improved, and the reliability of edge calculation has been improved.
Racial difference in mortality among COVID-19 hospitalizations in California
Authors: Rubens Muni , Ramamoorthy Venkataraghavan , Saxena Anshul , Zevallos Juan Carlos , Pelaez Juan Gabriel Ruiz , Ahmed Md Ashfaq , Zhang Zhenwei , McGranaghan Peter , Chaparro Sandra , Jimenez Javier 
Published: December 2023

AbstractIn the US, racial disparities in hospital outcomes are well documented. We explored whether race was associated with all-cause in-hospital mortality and intensive care unit (ICU) admission among COVID-19 patients in California. This was a retrospective analysis of California State Inpatient Database during 2020. Hospitalizations ≥ 18 years of age for COVID-19 were included. Cox proportional hazards with mixed effects were used for associations between race and in-hospital mortality. Logistic regression was used for the association between race and ICU admission. Among 87,934 COVID-19 hospitalizations, majority were Hispanics (56.5%), followed by White (27.3%), Asian, Pacific Islander, Native American (9.9%), and Black (6.3%). Cox regression showed higher mortality risk among Hispanics, compared to Whites (hazard ratio, 0.91; 95% CI 0.87–0.96), Blacks (hazard ratio, 0.87; 95% CI 0.79–0.94), and Asian, Pacific Islander, Native American (hazard ratio, 0.89; 95% CI 0.83–0.95). Logistic regression showed that the odds of ICU admission were significantly higher among Hispanics, compared to Whites (OR, 1.70; 95% CI 1.67–1.74), Blacks (OR, 1.70; 95% CI 1.64–1.78), and Asian, Pacific Islander, Native American (OR, 1.82; 95% CI 1.76–1.89). We found significant disparities in mortality among COVID-19 hospitalizations in California. Hispanics were the worst affected with the highest mortality and ICU admission rates.
Evaluating the antioxidant potential of resveratrol-gold nanoparticles in preventing oxidative stress in endothelium on a chip
Authors: Fayazbakhsh Farzaneh , Hataminia Fatemeh , Eslam Houra Mobaleghol , Ajoudanian Mohammad , Kharrazi Sharmin , Sharifi Kazem , Ghanbari Hossein 
Published: December 2023

AbstractVascular endothelial cells play a vital role in the health and maintenance of vascular homeostasis, but hyperglycemia disrupts their function by increasing cellular oxidative stress. Resveratrol, a plant polyphenol, possesses antioxidant properties that can mitigate oxidative stress. Addressing the challenges of its limited solubility and stability, gold nanoparticles (GNps) were utilized as carriers. A microfluidic chip (MFC) with dynamic flow conditions was designed to simulate body vessels and to investigate the antioxidant properties of resveratrol gold nanoparticles (RGNps), citrate gold nanoparticles (CGNps), and free Resveratrol on human umbilical vein endothelial cells (HUVEC). The 2, 2-diphenyl-1-picrylhydrazyl (DPPH) assay was employed to measure the extracellular antioxidant potential, and cell viability was determined using the Alamar Blue test. For assessing intracellular oxidative stress, the 2′,7′-dichlorodihydrofluorescein diacetate (DCFH-DA) assay was conducted, and results from both the cell culture plate and MFC were compared. Free Resveratrol demonstrated peak DPPH scavenging activity but had a cell viability of about 24–35%. RGNPs, both 3.0 ± 0.5 nm and 20.2 ± 4.7 nm, consistently showed high cell viability (more than about 90%) across tested concentrations. Notably, RGNPs (20 nm) exhibited antioxidative properties through DPPH scavenging activity (%) in the range of approximately 38–86% which was greater than that of CGNps at about 21–32%. In the MFC,the DCFH-DA analysis indicated that RGNPs (20 nm) reduced cellular oxidative stress by 57–82%, surpassing both CGNps and free Resveratrol. Morphologically, cells in the MFC presented superior structure compared to those in traditional cell culture plates, and the induction of hyperglycemia successfully led to the formation of multinucleated variant endothelial cells (MVECs). The MFC provides a distinct advantage in observing cell morphology and inducing endothelial cell dysfunction. RGNps have demonstrated significant potential in alleviating oxidative stress and preventing endothelial cell disorders.
An investigation on humans’ sensitivity to environmental temperature
Authors: Battistel Laura , Vilardi Andrea , Zampini Massimiliano , Parin Riccardo 
Published: December 2023

AbstractWhile earlier investigations into thermal perception focused on measuring the detection of temperature changes across distinct bodily regions, the complex nature of thermal perception throughout the entire body remains a subject of ongoing exploration. To address this, we performed an experiment using four climate chambers with oscillating temperatures between 24 °C ± 1 °C. Our study involved 26 participants who moved between these chambers and had the task of reporting whether the second chamber entered was warmer or colder than the previous one. We collected 3120 temperature judgments, which we analysed via generalised linear mixed-effects models. The results showed surprisingly accurate temperature discrimination abilities and limited variation between individuals. Specifically, the Point of Subjective Equality stood at − 0.13 °C (± 0.02 °C), the Just Noticeable Difference (JND) was 0.38 °C (± 0.02 °C), the JND95 (indicating 95% accuracy) 0.92 °C (± 0.05 °C), the negative ceiling performance level (CPL) was − 0.91 °C (± 0.28 °C) and the positive CPL 0.80 °C (± 0.34 °C). The implications of the JND95 and the CPLs are particularly noteworthy, as they hold potential to significantly contribute to the advancement of intelligent algorithms for temperature control systems within building environments.