bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sea level extremes and compounding marine heatwaves in coastal Indonesia
Authors: Han Weiqing , Zhang Lei , Meehl Gerald A. , Kido Shoichiro , Tozuka Tomoki , Li Yuanlong , McPhaden Michael J. , Hu Aixue , Cazenave Anny , Rosenbloom Nan , Strand Gary , West B. Jason , Xing Wen 
Published: October 2022

AbstractLow-lying island nations like Indonesia are vulnerable to sea level Height EXtremes (HEXs). When compounded by marine heatwaves, HEXs have larger ecological and societal impact. Here we combine observations with model simulations, to investigate the HEXs and Compound Height-Heat Extremes (CHHEXs) along the Indian Ocean coast of Indonesia in recent decades. We find that anthropogenic sea level rise combined with decadal climate variability causes increased occurrence of HEXs during 2010–2017. Both HEXs and CHHEXs are driven by equatorial westerly and longshore northwesterly wind anomalies. For most HEXs, which occur during December-March, downwelling favorable northwest monsoon winds are enhanced but enhanced vertical mixing limits surface warming. For most CHHEXs, wind anomalies associated with a negative Indian Ocean Dipole (IOD) and co-occurring La Niña weaken the southeasterlies and cooling from coastal upwelling during May-June and November-December. Our findings emphasize the important interplay between anthropogenic warming and climate variability in affecting regional extremes.
Transient inhibition of p53 enhances prime editing and cytosine base-editing efficiencies in human pluripotent stem cells
Authors: Li Mu , Zhong Aaron , Wu Youjun , Sidharta Mega , Beaury Michael , Zhao Xiaolan , Studer Lorenz , Zhou Ting 
Published: October 2022

AbstractPrecise gene editing in human pluripotent stem cells (hPSCs) holds great promise for studying and potentially treating human diseases. Both prime editing and base editing avoid introducing double strand breaks, but low editing efficiencies make those techniques still an arduous process in hPSCs. Here we report that co-delivering of p53DD, a dominant negative fragment of p53, can greatly enhance prime editing and cytosine base editing efficiencies in generating precise mutations in hPSCs. We further apply PE3 in combination with p53DD to efficiently create multiple isogenic hPSC lines, including lines carrying GBA or LRRK2 mutations associated with Parkinson disease and a LMNA mutation linked to Hutchinson-Gilford progeria syndrome. We also correct GBA and LMNA mutations in the patient-specific iPSCs. Our data show that p53DD improves PE3 efficiency without compromising the genome-wide safety, making it feasible for safe and routine generation of isogenic hPSC lines for disease modeling.
Molecular insights into DNA recognition and methylation by non-canonical type I restriction-modification systems
Authors: Zhu Jingpeng , Gao Yina , Wang Yong , Zhan Qi , Feng Han , Luo Xiu , Li Peipei , Liu Songqing , Hou Hai , Gao Pu 
Published: October 2022

AbstractType I restriction-modification systems help establish the prokaryotic DNA methylation landscape and provide protection against invasive DNA. In addition to classical m6A modifications, non-canonical type I enzymes catalyze both m6A and m4C using alternative DNA-modification subunits M1 and M2. Here, we report the crystal structures of the non-canonical PacII_M1M2S methyltransferase bound to target DNA and reaction product S-adenosylhomocysteine in a closed clamp-like conformation. Target DNA binds tightly within the central tunnel of the M1M2S complex and forms extensive contacts with all three protein subunits. Unexpectedly, while the target cytosine properly inserts into M2’s pocket, the target adenine (either unmethylated or methylated) is anchored outside M1’s pocket. A unique asymmetric catalysis is established where PacII_M1M2S has precisely coordinated the relative conformations of different subunits and evolved specific amino acids within M2/M1. This work provides insights into mechanisms of m6A/m4C catalysis and guidance for designing tools based on type I restriction-modification enzymes.
Human mtRF1 terminates COX1 translation and its ablation induces mitochondrial ribosome-associated quality control
Authors: Nadler Franziska , Lavdovskaia Elena , Krempler Angelique , Cruz-Zaragoza Luis Daniel , Dennerlein Sven , Richter-Dennerlein Ricarda 
Published: October 2022

AbstractTranslation termination requires release factors that read a STOP codon in the decoding center and subsequently facilitate the hydrolysis of the nascent peptide chain from the peptidyl tRNA within the ribosome. In human mitochondria eleven open reading frames terminate in the standard UAA or UAG STOP codon, which can be recognized by mtRF1a, the proposed major mitochondrial release factor. However, two transcripts encoding for COX1 and ND6 terminate in the non-conventional AGA or AGG codon, respectively. How translation termination is achieved in these two cases is not known. We address this long-standing open question by showing that the non-canonical release factor mtRF1 is a specialized release factor that triggers COX1 translation termination, while mtRF1a terminates the majority of other mitochondrial translation events including the non-canonical ND6. Loss of mtRF1 leads to isolated COX deficiency and activates the mitochondrial ribosome-associated quality control accompanied by the degradation of COX1 mRNA to prevent an overload of the ribosome rescue system. Taken together, these results establish the role of mtRF1 in mitochondrial translation, which had been a mystery for decades, and lead to a comprehensive picture of translation termination in human mitochondria.
Synthesized spatiotemporal mode-locking and photonic flywheel in multimode mesoresonators
Authors: Nie Mingming , Jia Kunpeng , Xie Yijun , Zhu Shining , Xie Zhenda , Huang Shu-Wei 
Published: October 2022

AbstractDissipative Kerr soliton (DKS) frequency combs—also known as microcombs—have arguably created a new field in cavity nonlinear photonics, with a strong cross-fertilization between theoretical, experimental, and technological research. Spatiotemporal mode-locking (STML) not only adds new degrees of freedom to ultrafast laser technology, but also provides new insights for implementing analogue computers and heuristic optimizers with photonics. Here, we combine the principles of DKS and STML to demonstrate the STML DKS by developing an unexplored ultrahigh-quality-factor Fabry–Pérot (FP) mesoresonator based on graded index multimode fiber (GRIN-MMF). Complementing the two-step pumping scheme with a cavity stress tuning method, we can selectively excite either the eigenmode DKS or the STML DKS. Furthermore, we demonstrate an ultralow noise microcomb that enhances the photonic flywheel performance in both the fundamental comb linewidth and DKS timing jitter. The demonstrated fundamental comb linewidth of 400 mHz and DKS timing jitter of 500 attosecond (averaging times up to 25 μs) represent improvements of 25× and 2.5×, respectively, from the state-of-the-art. Our results show the potential of GRIN-MMF FP mesoresonators as an ideal testbed for high-dimensional nonlinear cavity dynamics and photonic flywheel with ultrahigh coherence and ultralow timing jitter.
Endothelial alpha globin is a nitrite reductase
Authors: Keller T. C. Stevenson , Lechauve Christophe , Keller Alexander S. , Broseghini-Filho Gilson Brás , Butcher Joshua T. , Askew Page Henry R. , Islam Aditi , Tan Zhe Yin , DeLalio Leon J. , Brooks Steven , Sharma Poonam , Hong Kwangseok , Xu Wenhao , Padilha Alessandra Simão , Ruddiman Claire A. , Best Angela K. , Macal Edgar , Kim-Shapiro Daniel B. , Christ George , Yan Zhen , Cortese-Krott Miriam M. , Ricart Karina , Patel Rakesh , Bender Timothy P. , Sonkusare Swapnil K. , Weiss Mitchell J. , Ackerman Hans , Columbus Linda , Isakson Brant E. 
Published: October 2022

AbstractResistance artery vasodilation in response to hypoxia is essential for matching tissue oxygen and demand. In hypoxia, erythrocytic hemoglobin tetramers produce nitric oxide through nitrite reduction. We hypothesized that the alpha subunit of hemoglobin expressed in endothelium also facilitates nitrite reduction proximal to smooth muscle. Here, we create two mouse strains to test this: an endothelial-specific alpha globin knockout (EC Hba1Δ/Δ) and another with an alpha globin allele mutated to prevent alpha globin’s inhibitory interaction with endothelial nitric oxide synthase (Hba1WT/Δ36–39). The EC Hba1Δ/Δ mice had significantly decreased exercise capacity and intracellular nitrite consumption in hypoxic conditions, an effect absent in Hba1WT/Δ36–39 mice. Hypoxia-induced vasodilation is significantly decreased in arteries from EC Hba1Δ/Δ, but not Hba1WT/Δ36–39 mice. Hypoxia also does not lower blood pressure in EC Hba1Δ/Δ mice. We conclude the presence of alpha globin in resistance artery endothelium acts as a nitrite reductase providing local nitric oxide in response to hypoxia.
Genomic signatures associated with maintenance of genome stability and venom turnover in two parasitoid wasps
Authors: Ye Xinhai , Yang Yi , Zhao Can , Xiao Shan , Sun Yu H. , He Chun , Xiong Shijiao , Zhao Xianxin , Zhang Bo , Lin Haiwei , Shi Jiamin , Mei Yang , Xu Hongxing , Fang Qi , Wu Fei , Li Dunsong , Ye Gongyin 
Published: October 2022

AbstractParasitoid wasps are rapidly developing as a model for evolutionary biology. Here we present chromosomal genomes of two Anastatus wasps, A. japonicus and A. fulloi, and leverage these genomes to study two fundamental questions—genome size evolution and venom evolution. Anastatus shows a much larger genome than is known among other wasps, with unexpectedly recent bursts of LTR retrotransposons. Importantly, several genomic innovations, including Piwi gene family expansion, ubiquitous Piwi expression profiles, as well as transposable element-piRNA coevolution, have likely emerged for transposable element silencing to maintain genomic stability. Additionally, we show that the co-option evolution arose by expression shifts in the venom gland plays a dominant role in venom turnover. We also highlight the potential importance of non-venom genes that are coexpressed with venom genes during venom evolution. Our findings greatly advance the current understanding of genome size evolution and venom evolution, and these genomic resources will facilitate comparative genomics studies of insects in the future.
Targeting vasoactive intestinal peptide-mediated signaling enhances response to immune checkpoint therapy in pancreatic ductal adenocarcinoma
Authors: Ravindranathan Sruthi , Passang Tenzin , Li Jian-Ming , Wang Shuhua , Dhamsania Rohan , Ware Michael Brandon , Zaidi Mohammad Y. , Zhu Jingru , Cardenas Maria , Liu Yuan , Gumber Sanjeev , Robinson Brian , Sen-Majumdar Anish , Zhang Hanwen , Chandrakasan Shanmuganathan , Kissick Haydn , Frey Alan B. , Thomas Susan N. , El-Rayes Bassel F. , Lesinski Gregory B. , Waller Edmund K. 
Published: October 2022

AbstractA paucity of effector T cells within tumors renders pancreatic ductal adenocarcinoma (PDAC) resistant to immune checkpoint therapies. While several under-development approaches target immune-suppressive cells in the tumor microenvironment, there is less focus on improving T cell function. Here we show that inhibiting vasoactive intestinal peptide receptor (VIP-R) signaling enhances anti-tumor immunity in murine PDAC models. In silico data mining and immunohistochemistry analysis of primary tumors indicate overexpression of the neuropeptide vasoactive intestinal peptide (VIP) in human PDAC tumors. Elevated VIP levels are also present in PDAC patient plasma and supernatants of cultured PDAC cells. Furthermore, T cells up-regulate VIP receptors after activation, identifying the VIP signaling pathway as a potential target to enhance T cell function. In mouse PDAC models, VIP-R antagonist peptides synergize with anti-PD-1 antibody treatment in improving T cell recruitment into the tumors, activation of tumor-antigen-specific T cells, and inhibition of T cell exhaustion. In contrast to the limited single-agent activity of anti-PD1 antibodies or VIP-R antagonist peptides, combining both therapies eliminate tumors in up to 40% of animals. Furthermore, tumor-free mice resist tumor re-challenge, indicating anti-cancer immunological memory generation. VIP-R signaling thus represents a tumor-protective immune-modulatory pathway that is targetable in PDAC.
Modeling intercellular communication in tissues using spatial graphs of cells
Authors: Fischer David S. , Schaar Anna C. , Theis Fabian J. 
Published: October 2022

AbstractModels of intercellular communication in tissues are based on molecular profiles of dissociated cells, are limited to receptor–ligand signaling and ignore spatial proximity in situ. We present node-centric expression modeling, a method based on graph neural networks that estimates the effects of niche composition on gene expression in an unbiased manner from spatial molecular profiling data. We recover signatures of molecular processes known to underlie cell communication.
Mapping neurotransmitter systems to the structural and functional organization of the human neocortex
Authors: Hansen Justine Y. , Shafiei Golia , Markello Ross D. , Smart Kelly , Cox Sylvia M. L. , Nørgaard Martin , Beliveau Vincent , Wu Yanjun , Gallezot Jean-Dominique , Aumont Étienne , Servaes Stijn , Scala Stephanie G. , DuBois Jonathan M. , Wainstein Gabriel , Bezgin Gleb , Funck Thomas , Schmitz Taylor W. , Spreng R. Nathan , Galovic Marian , Koepp Matthias J. , Duncan John S. , Coles Jonathan P. , Fryer Tim D. , Aigbirhio Franklin I. , McGinnity Colm J. , Hammers Alexander , Soucy Jean-Paul , Baillet Sylvain , Guimond Synthia , Hietala Jarmo , Bedard Marc-André , Leyton Marco , Kobayashi Eliane , Rosa-Neto Pedro , Ganz Melanie , Knudsen Gitte M. , Palomero-Gallagher Nicola , Shine James M. , Carson Richard E. , Tuominen Lauri , Dagher Alain , Misic Bratislav 
Published: October 2022

AbstractNeurotransmitter receptors support the propagation of signals in the human brain. How receptor systems are situated within macro-scale neuroanatomy and how they shape emergent function remain poorly understood, and there exists no comprehensive atlas of receptors. Here we collate positron emission tomography data from more than 1,200 healthy individuals to construct a whole-brain three-dimensional normative atlas of 19 receptors and transporters across nine different neurotransmitter systems. We found that receptor profiles align with structural connectivity and mediate function, including neurophysiological oscillatory dynamics and resting-state hemodynamic functional connectivity. Using the Neurosynth cognitive atlas, we uncovered a topographic gradient of overlapping receptor distributions that separates extrinsic and intrinsic psychological processes. Finally, we found both expected and novel associations between receptor distributions and cortical abnormality patterns across 13 disorders. We replicated all findings in an independently collected autoradiography dataset. This work demonstrates how chemoarchitecture shapes brain structure and function, providing a new direction for studying multi-scale brain organization.
Using CFD simulations to investigate the shear stress in hydrodynamic cavitation reactors coupled with experimental validation using colony count measurements
Authors: Polgár Máté , Agarwal Charu , Gogate Parag , Németh Gábor , Csóka Levente 
Published: October 2022

AbstractThe current work investigates the shear stress distribution in hydrodynamic cavitation reactors with two different geometries using CFD simulations. Venturi type (positive geometry) and bore (negative geometry) were used to induce cavitation. Experimental validation of the predictions from simulations was also conducted by calculating the reduction rate in the colony count of Legionella pneumophila, a pathogenic bacterial strain. Both the numerical and experimental studies revealed the significant influence of the shape of the cavitation-inducing geometry on the flow characteristics and the distribution of shear stress. The simulation data indicated high shear stress formation in the positive geometry as a venturi, with the cavitation ranges for the two reactors being far apart from each other. The experimental study also confirmed that the flow conditions in the venturi-type reactor were more favourable compared to the bore geometry, resulting in a bacterial reduction efficiency as high as 99.98%. It was clearly demonstrated that the geometry of the cavitating device plays a crucial role in deciding the shear stress and its efficacy for the desired applications as per the predictions of the simulation model validated by the experimental results.
Effects of different virtual reality technology driven dual-tasking paradigms on posture and saccadic eye movements in healthy older adults
Authors: Imaoka Yu , Flury Andri , Hauri Laura , de Bruin Eling D. 
Published: October 2022

AbstractPostural sway and eye movements are potential biomarkers for dementia screening. Assessing the two movements comprehensively could improve the understanding of complicated syndrome for more accurate screening. The purpose of this research is to evaluate the effects of comprehensive assessment in healthy older adults (OA), using a novel concurrent comprehensive assessment system consisting of stabilometer and virtual reality headset. 20 healthy OA (70.4 ± 4.9 years) were recruited. Using a cross-sectional study design, this study investigated the effects of various dual-tasking paradigms with integrated tasks of visuospatial memory (VM), spatial orientation (SO), and visual challenge on posture and saccades. Dual-task paradigms with VM and SO affected the saccadic eye movements significantly. Two highly intensive tests of anti-saccade with VM task and pro-saccade with SO task also influenced postural sway significantly. Strong associations were seen between postural sway and eye movements for the conditions where the two movements theoretically shared common neural pathways in the brain, and vice versa. This study suggests that assessing posture and saccades with the integrated tasks comprehensively and simultaneously could be useful to explain different functions of the brain. The results warrant a cross-sectional study in OA with and without dementia to explore differences between these groups.
Ramp-shaped neural tuning supports graded population-level representation of the object-to-scene continuum
Authors: Park Jeongho , Josephs Emilie , Konkle Talia 
Published: October 2022

AbstractWe can easily perceive the spatial scale depicted in a picture, regardless of whether it is a small space (e.g., a close-up view of a chair) or a much larger space (e.g., an entire class room). How does the human visual system encode this continuous dimension? Here, we investigated the underlying neural coding of depicted spatial scale, by examining the voxel tuning and topographic organization of brain responses. We created naturalistic yet carefully-controlled stimuli by constructing virtual indoor environments, and rendered a series of snapshots to smoothly sample between a close-up view of the central object and far-scale view of the full environment (object-to-scene continuum). Human brain responses were measured to each position using functional magnetic resonance imaging. We did not find evidence for a smooth topographic mapping for the object-to-scene continuum on the cortex. Instead, we observed large swaths of cortex with opposing ramp-shaped profiles, with highest responses to one end of the object-to-scene continuum or the other, and a small region showing a weak tuning to intermediate scale views. However, when we considered the population code of the entire ventral occipito-temporal cortex, we found smooth and linear representation of the object-to-scene continuum. Our results together suggest that depicted spatial scale information is encoded parametrically in large-scale population codes across the entire ventral occipito-temporal cortex.
Dynamic analysis and optimal control considering cross transmission and variation of information
Authors: Kang Sida , Hou Xilin , Hu Yuhan , Liu Hongyu 
Published: October 2022

AbstractCross-transmission of information has a profound influence on the progress of science and technology and the discipline integration in the field of education. In this work, knowledge gained from the viral recombination and variation in COVID-19 transmission is applied to information transmission. Virus recombination and virus variation are similar to the crossing and information fusion phenomena in information transmission. An S2I4MR model with information crossing and variation is constructed. Then, the local and global asymptotic stabilities of the information-free equilibrium and information-existence equilibrium are analyzed. Additionally, the basic reproduction number $$R_0$$

R
0

of the model is calculated. As such, an optimal control strategy is hereby proposed to promote the cross-transmission of information and generate variant information. The numerical simulations support the results of the theoretical analysis and the sensitivity of the system towards certain control parameters. In particular, the results show that strengthening information crossing promotes the generation of variant information. Furthermore, encouraging information exchange and enhancing education improve the generation of information crossing and information variation.
An aphid inspired metaheuristic optimization algorithm and its application to engineering
Authors: Liu Renyun , Zhou Ning , Yao Yifei , Yu Fanhua 
Published: October 2022

AbstractThe biologically inspired metaheuristic algorithm obtains the optimal solution by simulating the living habits or behavior characteristics of creatures in nature. It has been widely used in many fields. A new bio-inspired algorithm, Aphids Optimization Algorithm (AOA), is proposed in this paper. This algorithm simulates the foraging process of aphids with wings, including the generation of winged aphids, flight mood, and attack mood. Concurrently, the corresponding optimization models are presented according to the above phases. At the phase of the flight mood, according to the comprehensive influence of energy and the airflow, the individuals adaptively choose the flight mode to migrate; at the phase of attack mood, individuals use their sense of smell and vision to locate food sources for movement. Experiments on benchmark test functions and two classical engineering design problems, indicate that the desired AOA is more efficient than other metaheuristic algorithms.