bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Eastern Atlantic Basin Pathway for the Export of the North Atlantic Deep Waters
Authors: Zhai Yujia , Yang Jiayan , Wan Xiuquan , Zou Sijia 
Published: December 2021

AbstractThe North Atlantic deep water (NADW), according to the classic ocean circulation theory, moves southward as a deep western boundary current (DWBC) even though it may veer into interior and then rejoin DWBC when encountering regional circulation features, such as eddy‐driven recirculation. In potential vorticity dynamics, the eastern side of the Mid‐Atlantic Ridge (MAR) may provide a similar topographic support as the continental slope off the western boundary for a southward transport of NADW. In this article, we quantify the mean meridional NADW transports on both sides of the MAR using a data‐assimilated product and find that the flow in the eastern basin contributes about of the net southward transport of NADW from 50° to 35°N. Our study points to the importance of observing NADW transport variations on the eastern side of the MAR in order to monitor the transport strength of Atlantic Meridional Overturning Circulation.
Blended Dry and Hot Events Index for Monitoring Dry‐Hot Events Over Global Land Areas
Authors: Wu Haijiang , Su Xiaoling , Singh Vijay P. 
Published: December 2021

AbstractThe amplifying effects of disasters caused by compound dry and hot extremes (dry‐hot events) have attracted widespread attention. This study presents a novel Blended Dry and Hot Events Index (BDHI) considering various dry and hot conditions (i.e., dry/hot, dry/cool, wet/hot, and wet/cool conditions). BDHI was applied to monitor dry‐hot events over global land areas during the 1950–2019 period and its performance was compared against that of the Standardized Compound Event Indicator (SCEI), which includes certain unsatisfactory or unclear features. We found that BDHI comprehensively reflected the characteristics of meteorological drought and temperature anomalies in monitoring dry‐hot events. Many regions around the globe have been experiencing more severe dry‐hot events since the 1990s, especially Russia, the USA, China, India, Australia, southern Africa, Europe, and South America. The proposed index is expected to serve as a potential tool for monitoring dry‐hot events and will be useful for managing and mitigating associated risks.
Measurements of Energy Dissipation in the Electron Diffusion Region
Authors: Zhou Meng , Man Hengyan , Yang Yan , Zhong Zhihong , Deng Xiaohua 
Published: December 2021

AbstractAn outstanding question in magnetic reconnection is how the energy being dissipated in the diffusion region. This paper evaluates the quasi‐viscous dissipation in the electron diffusion region (EDR) at Earth's magnetopause by the observations from the Magnetospheric MultiScale mission. We compared two fluid parameters, J·Eˊ and Pi‐D, and found that J·Eˊ and Pi‐D have opposite signs in about half of the examined EDRs. The gyrotropic effect is more important than the nongyrotropic effect for the viscous dissipation in the diffusion region. One intriguing discovery is that electrons are cooled rather than heated in a large portion of the EDRs, with the compressional effect dominates over the viscous effect in electron thermodynamics. Enthalpy flux flowing into or out from the EDR greatly affect the electron entropy variation within the EDR. This study is an important step toward fully resolving the dissipation mystery in reconnection.
Seasonal Seismicity in the Lake Biwa Region of Central Japan Moderately Modulated by Lake Water Storage Changes
Authors: Xue Liang , Fu Yuning , Johnson Christopher W. , Otero Torres Jason J. , Shum C. K. , Bürgmann Roland 
Published: December 2021

AbstractSeasonal seismicity in Japan has been observed and attributed to variations induced by hydrological loading, as well as atmospheric and pore‐fluid pressure. We examine the seasonal variations of crustal (<15 km depth) and low magnitude (M < 4.5) earthquakes in central Japan near the Biwako‐Seigan Fault Zone (BSFZ), and analyze their correlation with the annual hydrological cycle of nearby Lake Biwa, the largest freshwater lake in Japan. The 2002–2018 lake water storage is estimated using water‐level gauge and satellite altimetry data. Regional surface mass loading from soil moisture and snow predicted by the Global Land Data Assimilation System is used to augment the lake mass variation. We compute the stress and stressing‐rate changes induced by the surface mass loading from lake storage, snow, and soil moisture at seismogenic depth (10 km) along the BSFZ using a finite element model incorporating a 3D Earth structure. The results show that seasonal surface mass loading generates 1–5 kPa peak‐to‐peak Coulomb stress change and 2.5–15 kPa/year stressing‐rate variations on the fault segments along the BSFZ. Two of the four fault segments present significant correlation between local seismicity rate and loading‐derived stress and/or stressing rate changes. Among the hydrological load components, lake water, snow, and soil moisture exhibit different annual phases, and the lake water storage dominates the total annual stress changes. Our analysis indicates that seasonal surface hydrological loads, especially lake water variations, modulate the seismicity rate along the BSFZ in central Japan.
Recoil Leader and Associated Discharge Features Observed During the Progression of a Multi‐Branched Upward Lightning Flash
Authors: Huang Haitao , Wang Daohong , Wu Ting , Takagi Nobuyuki 
Published: December 2021

AbstractUsing a high‐speed video camera and a high‐speed optical imaging system, we observed a multi‐branched upward lightning flash that exhibited several special discharge features. One special feature is that a series of recoil leaders and the subsequent discharges caused by the connection of some recoil leaders to a conducting channel could extend a discharge channel like a leader. Another special feature is that the subsequent discharge could be similar to either a return stroke (RS) or an M‐component or something between. It seems that when a recoil leader initiated in a more conductive channel with a closer distance to a conducting channel, its subsequent discharge is similar to an M‐component. In cases with opposite conditions, the subsequent discharge will become similar to a RS. In conditions between the above two cases, a discharge that is intermediate between the RS and M‐component will occur.
T cell receptor (TCR) signaling in health and disease
Authors: Shah Kinjal , Al-Haidari Amr , Sun Jianmin , Kazi Julhash U. 
Published: December 2021

AbstractInteraction of the T cell receptor (TCR) with an MHC-antigenic peptide complex results in changes at the molecular and cellular levels in T cells. The outside environmental cues are translated into various signal transduction pathways within the cell, which mediate the activation of various genes with the help of specific transcription factors. These signaling networks propagate with the help of various effector enzymes, such as kinases, phosphatases, and phospholipases. Integration of these disparate signal transduction pathways is done with the help of adaptor proteins that are non-enzymatic in function and that serve as a scaffold for various protein–protein interactions. This process aids in connecting the proximal to distal signaling pathways, thereby contributing to the full activation of T cells. This review provides a comprehensive snapshot of the various molecules involved in regulating T cell receptor signaling, covering both enzymes and adaptors, and will discuss their role in human disease.
Natural Language Processing markers in first episode psychosis and people at clinical high-risk
Authors: Morgan Sarah E. , Diederen Kelly , Vértes Petra E. , Ip Samantha H. Y. , Wang Bo , Thompson Bethany , Demjaha Arsime , De Micheli Andrea , Oliver Dominic , Liakata Maria , Fusar-Poli Paolo , Spencer Tom J. , McGuire Philip 
Published: December 2021

AbstractRecent work has suggested that disorganised speech might be a powerful predictor of later psychotic illness in clinical high risk subjects. To that end, several automated measures to quantify disorganisation of transcribed speech have been proposed. However, it remains unclear which measures are most strongly associated with psychosis, how different measures are related to each other and what the best strategies are to collect speech data from participants. Here, we assessed whether twelve automated Natural Language Processing markers could differentiate transcribed speech excerpts from subjects at clinical high risk for psychosis, first episode psychosis patients and healthy control subjects (total N = 54). In-line with previous work, several measures showed significant differences between groups, including semantic coherence, speech graph connectivity and a measure of whether speech was on-topic, the latter of which outperformed the related measure of tangentiality. Most NLP measures examined were only weakly related to each other, suggesting they provide complementary information. Finally, we compared the ability of transcribed speech generated using different tasks to differentiate the groups. Speech generated from picture descriptions of the Thematic Apperception Test and a story re-telling task outperformed free speech, suggesting that choice of speech generation method may be an important consideration. Overall, quantitative speech markers represent a promising direction for future clinical applications.
Vesicle shape transformations driven by confined active filaments
Authors: Peterson Matthew S. E. , Baskaran Aparna , Hagan Michael F. 
Published: December 2021

AbstractIn active matter systems, deformable boundaries provide a mechanism to organize internal active stresses. To study a minimal model of such a system, we perform particle-based simulations of an elastic vesicle containing a collection of polar active filaments. The interplay between the active stress organization due to interparticle interactions and that due to the deformability of the confinement leads to a variety of filament spatiotemporal organizations that have not been observed in bulk systems or under rigid confinement, including highly-aligned rings and caps. In turn, these filament assemblies drive dramatic and tunable transformations of the vesicle shape and its dynamics. We present simple scaling models that reveal the mechanisms underlying these emergent behaviors and yield design principles for engineering active materials with targeted shape dynamics.
Hyperbolic optics and superlensing in room-temperature KTN from self-induced k-space topological transitions
Authors: Gelkop Yehonatan , Di Mei Fabrizio , Frishman Sagi , Garcia Yehudit , Falsi Ludovica , Perepelitsa Galina , Conti Claudio , DelRe Eugenio , Agranat Aharon J. 
Published: December 2021

AbstractA hyperbolic medium will transfer super-resolved optical waveforms with no distortion, support negative refraction, superlensing, and harbor nontrivial topological photonic phases. Evidence of hyperbolic effects is found in periodic and resonant systems for weakly diffracting beams, in metasurfaces, and even naturally in layered systems. At present, an actual hyperbolic propagation requires the use of metamaterials, a solution that is accompanied by constraints on wavelength, geometry, and considerable losses. We show how nonlinearity can transform a bulk KTN perovskite into a broadband 3D hyperbolic substance for visible light, manifesting negative refraction and superlensing at room-temperature. The phenomenon is a consequence of giant electro-optic response to the electric field generated by the thermal diffusion of photogenerated charges. Results open new scenarios in the exploration of enhanced light-matter interaction and in the design of broadband photonic devices.
Cell-specific alterations in Pitx1 regulatory landscape activation caused by the loss of a single enhancer
Authors: Rouco Raquel , Bompadre Olimpia , Rauseo Antonella , Fazio Olivier , Peraldi Rodrigue , Thorel Fabrizio , Andrey Guillaume 
Published: December 2021

AbstractDevelopmental genes are frequently controlled by multiple enhancers sharing similar specificities. As a result, deletions of such regulatory elements have often failed to reveal their full function. Here, we use thePitx1testbed locus to characterize in detail the regulatory and cellular identity alterations following the deletion of one of its enhancers (Pen). By combining single cell transcriptomics and an in-embryo cell tracing approach, we observe an increased fraction ofPitx1non/low-expressing cells and a decreased fraction ofPitx1high-expressing cells. We find that the over-representation ofPitx1non/low-expressing cells originates from a failure of thePitx1locus to coordinate enhancer activities and 3D chromatin changes. This locusmis-activation induces a localized heterochrony and a concurrent loss of irregular connective tissue, eventually leading to a clubfoot phenotype. This data suggests that, in some cases, redundant enhancers may be used to locally enforce a robust activation of their host regulatory landscapes.
Comparison of potential drinking water source contamination across one hundred U.S. cities
Authors: Turner Sean W. D. , Rice Jennie S. , Nelson Kristian D. , Vernon Chris R. , McManamay Ryan , Dickson Kerim , Marston Landon 
Published: December 2021

AbstractDrinking water supplies of cities are exposed to potential contamination arising from land use and other anthropogenic activities in local and distal source watersheds. Because water quality sampling surveys are often piecemeal, regionally inconsistent, and incomplete with respect to unregulated contaminants, the United States lacks a detailed comparison of potential source water contamination across all of its large cities. Here we combine national-scale geospatial datasets with hydrologic simulations to compute two metrics representing potential contamination of water supplies from point and nonpoint sources for over a hundred U.S. cities. We reveal enormous diversity in anthropogenic activities across watersheds with corresponding disparities in the potential contamination of drinking water supplies to cities. Approximately 5% of large cities rely on water that is composed primarily of runoff from non-pristine lands (e.g., agriculture, residential, industrial), while four-fifths of all large cities that withdraw surface water are exposed to treated wastewater in their supplies.
Existence of a continental-scale river system in eastern Tibet during the late Cretaceous–early Palaeogene
Authors: Zhao Xudong , Zhang Huiping , Hetzel Ralf , Kirby Eric , Duvall Alison R. , Whipple Kelin X. , Xiong Jianguo , Li Yifei , Pang Jianzhang , Wang Ying , Wang Ping , Liu Kang , Ma Pengfei , Zhang Bo , Li Xuemei , Zhang Jiawei , Zhang Peizhen 
Published: December 2021

AbstractThe establishment of continental-scale drainage systems on Earth is largely controlled by topography related to plate boundary deformation and buoyant mantle. Drainage patterns of the great rivers in Asia are thought to be highly dynamic during the Cenozoic collision of India and Eurasia, but the drainage pattern and landscape evolution prior to the development of high topography in eastern Tibet remain largely unknown. Here we report the results of petro-stratigraphy, heavy-mineral analysis, and detrital zircon U-Pb dating from late Cretaceous–early Palaeogene sedimentary basin strata along the present-day eastern margin of the Tibetan Plateau. Similarities in the provenance signatures among basins indicate that a continental-scale fluvial system once drained southward into the Neo-Tethyan Ocean. These results challenge existing models of drainage networks that flowed toward the East Asian marginal seas and require revisions to inference of palaeo-topography during the Late Cretaceous. The presence of a continent-scale river may have provided a stable long-term base level which, in turn, facilitated the development of an extensive low-relief landscape that is preserved atop interfluves above the deeply incised canyons of eastern Tibet.
Cyclin/Forkhead-mediated coordination of cyclin waves: an autonomous oscillator rationalizing the quantitative model of Cdk control for budding yeast
Authors: Barberis Matteo 
Published: December 2021

AbstractNetworks of interacting molecules organize topology, amount, and timing of biological functions. Systems biology concepts required to pin down ‘network motifs’ or ‘design principles’ for time-dependent processes have been developed for the cell division cycle, through integration of predictive computer modeling with quantitative experimentation. A dynamic coordination of sequential waves of cyclin-dependent kinases (cyclin/Cdk) with the transcription factors network offers insights to investigate how incompatible processes are kept separate in time during the eukaryotic cell cycle. Here this coordination is discussed for the Forkhead transcription factors in light of missing gaps in the current knowledge of cell cycle control in budding yeast. An emergent design principle is proposed where cyclin waves are synchronized by a cyclin/Cdk-mediated feed-forward regulation through the Forkhead as a transcriptional timer. This design is rationalized by the bidirectional interaction between mitotic cyclins and the Forkhead transcriptional timer, resulting in an autonomous oscillator that may be instrumental for a well-timed progression throughout the cell cycle. The regulation centered around the cyclin/Cdk–Forkhead axis can be pivotal to timely coordinate cell cycle dynamics, thereby to actuate the quantitative model of Cdk control.
An open-access database and analysis tool for perovskite solar cells based on the FAIR data principles
Authors: Jacobsson T. Jesper , Hultqvist Adam , García-Fernández Alberto , Anand Aman , Al-Ashouri Amran , Hagfeldt Anders , Crovetto Andrea , Abate Antonio , Ricciardulli Antonio Gaetano , Vijayan Anuja , Kulkarni Ashish , Anderson Assaf Y. , Darwich Barbara Primera , Yang Bowen , Coles Brendan L. , Perini Carlo A. R. , Rehermann Carolin , Ramirez Daniel , Fairen-Jimenez David , Di Girolamo Diego , Jia Donglin , Avila Elena , Juarez-Perez Emilio J. , Baumann Fanny , Mathies Florian , González G. S. Anaya , Boschloo Gerrit , Nasti Giuseppe , Paramasivam Gopinath , Martínez-Denegri Guillermo , Näsström Hampus , Michaels Hannes , Köbler Hans , Wu Hua , Benesperi Iacopo , Dar M. Ibrahim , Bayrak Pehlivan Ilknur , Gould Isaac E. , Vagott Jacob N. , Dagar Janardan , Kettle Jeff , Yang Jie , Li Jinzhao , Smith Joel A. , Pascual Jorge , Jerónimo-Rendón Jose J. , Montoya Juan Felipe , Correa-Baena Juan-Pablo , Qiu Junming , Wang Junxin , Sveinbjörnsson Kári , Hirselandt Katrin , Dey Krishanu , Frohna Kyle , Mathies Lena , Castriotta Luigi A. , Aldamasy Mahmoud. H. , Vasquez-Montoya Manuel , Ruiz-Preciado Marco A. , Flatken Marion A. , Khenkin Mark V. , Grischek Max , Kedia Mayank , Saliba Michael , Anaya Miguel , Veldhoen Misha , Arora Neha , Shargaieva Oleksandra , Maus Oliver , Game Onkar S. , Yudilevich Ori , Fassl Paul , Zhou Qisen , Betancur Rafael , Munir Rahim , Patidar Rahul , Stranks Samuel D. , Alam Shahidul , Kar Shaoni , Unold Thomas , Abzieher Tobias , Edvinsson Tomas , David Tudur Wyn , Paetzold Ulrich W. , Zia Waqas , Fu Weifei , Zuo Weiwei , Schröder Vincent R. F. , Tress Wolfgang , Zhang Xiaoliang , Chiang Yu-Hsien , Iqbal Zafar , Xie Zhiqiang , Unger Eva 
Published: December 2021

AbstractLarge datasets are now ubiquitous as technology enables higher-throughput experiments, but rarely can a research field truly benefit from the research data generated due to inconsistent formatting, undocumented storage or improper dissemination. Here we extract all the meaningful device data from peer-reviewed papers on metal-halide perovskite solar cells published so far and make them available in a database. We collect data from over 42,400 photovoltaic devices with up to 100 parameters per device. We then develop open-source and accessible procedures to analyse the data, providing examples of insights that can be gleaned from the analysis of a large dataset. The database, graphics and analysis tools are made available to the community and will continue to evolve as an open-source initiative. This approach of extensively capturing the progress of an entire field, including sorting, interactive exploration and graphical representation of the data, will be applicable to many fields in materials science, engineering and biosciences.
CRISPR/Cas9-mediated base-editing enables a chain reaction through sequential repair of sgRNA scaffold mutations
Authors: Fukushima Tsuyoshi , Tanaka Yosuke , Adachi Keito , Masuyama Nanami , Tsuchiya Akiho , Asada Shuhei , Ishiguro Soh , Mori Hideto , Seki Motoaki , Yachie Nozomu , Goyama Susumu , Kitamura Toshio 
Published: December 2021

AbstractCell behavior is controlled by complex gene regulatory networks. Although studies have uncovered diverse roles of individual genes, it has been challenging to record or control sequential genetic events in living cells. In this study, we designed two cellular chain reaction systems that enable sequential sgRNA activation in mammalian cells using a nickase Cas9 tethering of a cytosine nucleotide deaminase (nCas9-CDA). In these systems, thymidine (T)-to-cytosine (C) substitutions in the scaffold region of the sgRNA or the TATA box-containing loxP sequence (TATAloxP) are corrected by the nCas9-CDA, leading to activation of the next sgRNA. These reactions can occur multiple times, resulting in cellular chain reactions. As a proof of concept, we established a chain reaction by repairing sgRNA scaffold mutations in 293 T cells. Importantly, the results obtained in yeast or in vitro did not match those obtained in mammalian cells, suggesting that in vivo chain reactions need to be optimized in appropriate cellular contexts. Our system may lay the foundation for building cellular chain reaction systems that have a broad utility in the future biomedical research.
Nutrient metabolism in the liver and muscle of juvenile blunt snout bream (Megalobrama amblycephala) in response to dietary methionine levels
Authors: Ji Ke , Liang Hualiang , Ren Mingchun , Ge Xianping , Pan Liangkun , Yu Heng 
Published: December 2021

AbstractA 75-day rearing trial was designed to study the response of juvenile Megalobrama amblycephala to dietary methionine (Met) levels. Three practical diets with graded Met levels (0.40%, 0.84% and 1.28% dry matter) were prepared to feed the juvenile fish. The results showed that the 0.84% Met diet significantly improved the growth compared with 0.40% diets. Compared with 0.84% and 1.28% Met, 0.40% Met significantly increased the hepatic lipid content, while decreasing the muscular lipid and glycogen contents. 0.40% Met decreased the protein levels of phospho-Eukaryotic initiation factor 4E binding protein-1 (p-4e-bp1), 4e-bp1 and Ribosomal protein S6 kinase 1 in the liver, compared with 0.84% diet, while an increasing trend was observed in the muscle. Met supplementation tended to decrease and increase lipid synthesis in the liver and muscle, respectively, via changing mRNA levels of sterol regulatory element-binding protein 1, fatty acid synthetase and acetyl-CoA carboxylase. 1.28% dietary Met promoted fatty acid β-oxidation and lipolysis in both the liver and muscle by increasing carnitine palmitoyl transferase 1, peroxisome proliferator activated receptor alpha, lipoprotein lipase and lipase mRNA levels. Compared with 0.40% and 0.84% dietary Met, 1.28% Met enhanced the mRNA levels of hepatic gluconeogenesis related genes phosphoenolpyruvate carboxykinase (pepck), and glucose-6-phosphatase, and muscular glycolysis related genes phosphofructokinase (pfk), and pyruvate kinase (pk). The mRNA levels of hepatic pfk, pk and glucokinase were markedly downregulated by 1.28% Met compared with 0.84% level. Muscular pepck, glycogen synthase, and hepatic glucose transporters 2 mRNA levels were induced by 1.28% Met. Generally, deficient Met level decreased the growth of juvenile Megalobrama amblycephala, and the different nutrient metabolism responses to dietary Met were revealed in the liver and muscle.