bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unified Theory of the Arc Auroras: Formation Mechanism of the Arc Auroras Conforming General Principles of Convection and FAC Generation
Authors: Tanaka T. , Watanabe M. , Ebihara Y. , Fujita S. , Nishitani N. , Kataoka R. 
Published: August 2022

AbstractThe arc aurora can be considered as the visualization of the field‐aligned current (FAC). In various cases, the numerically reproduced FAC morphologically matches well with that of the observed arc aurora. Such example can be seen in the sun‐aligned arc, the fan arc, and the theta aurora under the northward interplanetary magnetic field (IMF), and the substorm, the quiet arc, and the initial brightening under the southward IMF. The FAC reproduced by the global simulation is based on the general principle of the magnetohydrodynamic (MHD). In such general principle, the FAC is transmission of net charge, net charge is divE, and E is equivalent to motion. After all, the FAC is transmission of convection motion. In order to transmit the FAC to the dissipative ionosphere based on the MHD, formations of the dynamo and shear that leads from the magnetosphere to the ionosphere are essential. The dynamo and shear are reproduced so as to properly match with each convection structure. The comparison under various magnetospheric topologies between the global simulation and the arc aurora observation indicates that the arc aurora and the FAC occurs inevitably controlled by convection structure. Such a principle of the FAC and convection holds even for the onset FAC.
Accounting for Topographic Effects on Snow Cover Fraction and Surface Albedo Simulations Over the Tibetan Plateau in Winter
Authors: Miao Xin , Guo Weidong , Qiu Bo , Lu Sha , Zhang Yu , Xue Yongkang , Sun Shufen 
Published: August 2022

AbstractThe Tibetan Plateau (TP) is the highest land in the world and has a very complex topography. However, the influence of topography on TP snow cover simulations has not been adequately addressed in most land surface models. The analysis of satellite observations indicates that snow cover fraction (SCF) simulation biases increase with the topography complexity, and this increasing trend slows down when the standard deviation of topography is greater than 200 m. The result also shows that using the SCF schemes without consideration of topography leads to a consistent overestimation in winter. To account for the topographic effects, we introduce a modified topographic factor to the SCF schemes. Then we conduct regional simulations using the Simplified Simple Biosphere Model version 3 (SSiB3) and evaluate the results at the location of observation sites to reduce the uncertainty induced by forcing data. Compared with the default SCF scheme, the mean winter SCF bias is reduced from 3.83% to −0.10%. The optimization of SCF simulations further improves the winter surface albedo and land surface temperature (LST) simulations. The winter surface albedo bias over the TP is reduced from 0.020 to 0.007, with a maximum reduction by −0.133. The winter LST bias is reduced from −3.33 to −3.04 K, with a maximum reduction by 3.60 K. This study highlights the importance of topographic effects in simulating snow cover distribution and land surface energy budget for reducing the “cold bias” in winter climate simulations over the TP.
Biotic and Paleoceanographic Changes Across the Late Cretaceous Oceanic Anoxic Event 2 in the Southern High Latitudes (IODP Sites U1513 and U1516, SE Indian Ocean)
Authors: Petrizzo Maria Rose , Amaglio Giulia , Watkins David K. , MacLeod Kenneth G. , Huber Brian T. , Hasegawa Takashi , Wolfgring Erik 
Published: August 2022

AbstractOceanic Anoxic Event 2, spanning the Cenomanian/Turonian boundary (93.9 Ma), was an episode of major perturbations in the global carbon cycle. To investigate the response of biota and the paleoceanographic conditions across this event, we present data from International Ocean Discovery Program sites U1513 and U1516 in the Mentelle Basin (offshore SW Australia; paleolatitude 59°–60°S in the mid‐Cretaceous) that register the first complete records of OAE 2 at southern high latitudes. Calcareous nannofossils provide a reliable bio‐chronostratigraphic framework. The distribution and abundance patterns of planktonic and benthic foraminifera, radiolaria, and calcispheres permit interpretation of the dynamics of the water mass stratification and provide support for the paleobathymetric reconstruction of the two sites, with Site U1513 located northwest of the Mentelle Basin depocenter and at a deeper depth than Site U1516. The lower OAE 2 interval is characterized by reduced water mass stratification with alternating episodes of enhanced surface water productivity and variations of the thickness of the mixed layer as indicated by the fluctuations in abundance of the intermediate dwelling planktonic foraminifera. The middle OAE 2 interval contains lithologies composed almost entirely of radiolaria reflecting extremely high marine productivity; the low CaCO3 content is consistent with marked shoaling of the Carbonate Compensation Depth and ocean acidification because of CaCO3 undersaturation. Conditions moderated after deposition of the silica‐rich, CaCO3‐poor rocks as reflected by the microfossil changes indicating a relatively stable water column although episodes of enhanced eutrophy did continue into the lower Turonian at Site U1516.
Intratumoral PD-1+CD8+ T cells associate poor clinical outcomes and adjuvant chemotherapeutic benefit in gastric cancer
Authors: Yu Kuan , Gu Yun , Zhang Puran , Fang Hanji , Cao Yifan , Wang Jieti , Lin Chao , Liu Hao , Zhang Heng , He Hongyong , Li Ruochen , Qin Jing , Li He , Xu Jiejie 
Published: August 2022

Abstract
Background
Although PD-1 has been reported to be a marker of T-cell exhaustion in several malignancies, the biological role of PD-1+CD8+ T cells in gastric cancer (GC) remains unclear. Herein, we aimed to investigate the role of PD-1+CD8+ T cells in the tumour microenvironment and its clinical significance in GC.

Designs
This study included 441 tumour microarray specimens and 60 Flow cytometry specimens of GC patients from Zhongshan Hospital, and 250 GC patients from the Asian Cancer Research Group.

Results
Here, we demonstrated that PD-1+CD8+ T cells functioned as an independent adverse prognosticator in GC. In addition, an abundance of intratumoral PD-1+CD8+ T cells indicated worse chemotherapeutic responsiveness to fluorouracil in Stage III GC patients. Mechanistically, PD-1+CD8+ T cell high infiltration indicated an exhausted phenotype of global CD8+ T cells in GC tissues, which was characterised by elevated immune checkpoint expression including CTLA-4 and TIM-3, whereas decreased expression of perforin. Furthermore, PD-1+CD8+ T cell high-infiltration patients with Stage III GC held elevated activity of several therapeutic signal pathways.

Conclusions
Our study highlighted that PD-1+CD8+ T cell abundance predicts inferior prognosis in GC, and may serve as a novel predictive biomarker to guide therapeutic option.
Inelastic phonon transport across atomically sharp metal/semiconductor interfaces
Authors: Li Qinshu , Liu Fang , Hu Song , Song Houfu , Yang Susu , Jiang Hailing , Wang Tao , Koh Yee Kan , Zhao Changying , Kang Feiyu , Wu Junqiao , Gu Xiaokun , Sun Bo , Wang Xinqiang 
Published: August 2022

AbstractUnderstanding thermal transport across metal/semiconductor interfaces is crucial for the heat dissipation of electronics. The dominant heat carriers in non-metals, phonons, are thought to transport elastically across most interfaces, except for a few extreme cases where the two materials that formed the interface are highly dissimilar with a large difference in Debye temperature. In this work, we show that even for two materials with similar Debye temperatures (Al/Si, Al/GaN), a substantial portion of phonons will transport inelastically across their interfaces at high temperatures, significantly enhancing interface thermal conductance. Moreover, we find that interface sharpness strongly affects phonon transport process. For atomically sharp interfaces, phonons are allowed to transport inelastically and interface thermal conductance linearly increases at high temperatures. With a diffuse interface, inelastic phonon transport diminishes. Our results provide new insights on phonon transport across interfaces and open up opportunities for engineering interface thermal conductance specifically for materials of relevance to microelectronics.
Flavin-enabled reductive and oxidative epoxide ring opening reactions
Authors: De Bidhan Chandra , Zhang Wenjun , Yang Chunfang , Mándi Attila , Huang Chunshuai , Zhang Liping , Liu Wei , Ruszczycky Mark W. , Zhu Yiguang , Ma Ming , Bashiri Ghader , Kurtán Tibor , Liu Hung-wen , Zhang Changsheng 
Published: August 2022

AbstractEpoxide ring opening reactions are common and important in both biological processes and synthetic applications and can be catalyzed in a non-redox manner by epoxide hydrolases or reductively by oxidoreductases. Here we report that fluostatins (FSTs), a family of atypical angucyclines with a benzofluorene core, can undergo nonenzyme-catalyzed epoxide ring opening reactions in the presence of flavin adenine dinucleotide (FAD) and nicotinamide adenine dinucleotide (NADH). The 2,3-epoxide ring in FST C is shown to open reductively via a putative enol intermediate, or oxidatively via a peroxylated intermediate with molecular oxygen as the oxidant. These reactions lead to multiple products with different redox states that possess a single hydroxyl group at C-2, a 2,3-vicinal diol, a contracted five-membered A-ring, or an expanded seven-membered A-ring. Similar reactions also take place in both natural products and other organic compounds harboring an epoxide adjacent to a carbonyl group that is conjugated to an aromatic moiety. Our findings extend the repertoire of known flavin chemistry that may provide new and useful tools for organic synthesis.
Codoped porous carbon nanofibres as a potassium metal host for nonaqueous K-ion batteries
Authors: Li Siwu , Zhu Haolin , Liu Yuan , Han Zhilong , Peng Linfeng , Li Shuping , Yu Chuang , Cheng Shijie , Xie Jia 
Published: August 2022

AbstractPotassium metal is an appealing alternative to lithium as an alkali metal anode for future electrochemical energy storage systems. However, the use of potassium metal is hindered by the growth of unfavourable deposition (e.g., dendrites) and volume changes upon cycling. To circumvent these issues, we propose the synthesis and application of nitrogen and zinc codoped porous carbon nanofibres that act as potassium metal hosts. This carbonaceous porous material enables rapid potassium infusion (e.g., < 1 s cm−2) with a high potassium content (e.g., 97 wt. %) and low potassium nucleation overpotential (e.g., 15 mV at 0.5 mA cm−2). Experimental and theoretical measurements and analyses demonstrate that the carbon nanofibres induce uniform potassium deposition within its porous network and facilitate a dendrite-free morphology during asymmetric and symmetric cell cycling. Interestingly, when the potassium-infused carbon material is tested as an active negative electrode material in combination with a sulfur-based positive electrode and a nonaqueous electrolyte solution in the coin cell configuration, an average discharge voltage of approximately 1.6 V and a discharge capacity of approximately 470 mA h g−1 after 600 cycles at 500 mA g−1 and 25 °C are achieved.
Triple negative breast cancer: Pitfalls and progress
Authors: Zagami Paola , Carey Lisa Anne 
Published: August 2022

AbstractTriple negative breast cancer (TNBC) is characterized by the lack of estrogen and progesterone receptor expression and lacks HER2 overexpression or gene amplification. It accounts for 10–15% of incident breast cancers and carries the worst prognosis. TNBC is overrepresented among Black and pre-menopausal women and is associated with significant psychological and treatment-related burdens, including financial toxicity. Like other breast cancers, TNBC is biologically heterogeneous, leading to diverse clinical and epidemiological behaviors, however, unlike the other clinical subtypes, in TNBC we still lack tumor-specific targeted therapy. Early TNBC outcomes have improved due to the intensification of therapies, including improvements in polychemotherapy and the addition of immunotherapy. Future efforts are needed to identify targetable aberrations for specific drug therapy, prevent immune evasion, and increase social-economic support. Given that the name TNBC illustrates its lack of specifically targeted and effective therapy, we look forward to being able to retire the name in favor of a group of targetable entities within what is now called “TNBC”.
Revealing the topological phase diagram of ZrTe5 using the complex strain fields of microbubbles
Authors: Tajkov Zoltán , Nagy Dániel , Kandrai Konrád , Koltai János , Oroszlány László , Süle Péter , Horváth Zsolt E. , Vancsó Péter , Tapasztó Levente , Nemes-Incze Péter 
Published: August 2022

AbstractTopological materials host robust properties, unaffected by microscopic perturbations, owing to the global topological properties of the bulk electron system. Materials in which the topological invariant can be changed by easily tuning external parameters are especially sought after. Zirconium pentatelluride (ZrTe5) is one of a few experimentally available materials that reside close to the boundary of a topological phase transition, allowing the switching of its invariant by mechanical strain. Here, we unambiguously identify a topological insulator–metal transition as a function of strain, by a combination of ab initio calculations and direct measurements of the local charge density. Our model quantitatively describes the response to complex strain patterns found in bubbles of few layer ZrTe5without fitting parameters, reproducing the mechanical deformation-dependent closing of the band gap observed using scanning tunneling microscopy. We calculate the topological phase diagram of ZrTe5and identify the phase at equilibrium, enabling the design of device architectures, which exploit the topological switching characteristics of the system.
Pettifor maps of complex ternary two-dimensional transition metal sulfides
Authors: Silva Andrea , Cao Jiangming , Polcar Tomas , Kramer Denis 
Published: August 2022

AbstractAlloying is an established strategy to tune the properties of bulk compounds for desired applications. With the advent of nanotechnology, the same strategy can be applied to 2D materials for technological applications, like single-layer transistors and solid lubricants. Here we present a systematic analysis of the phase behaviour of substitutional 2D alloys in the Transition Metal Disulfides (TMD) family. The phase behaviour is quantified in terms of a metastability metric and benchmarked against many-body expansion of the energy landscape. We show how the metastability metric can be directly used as starting point for setting up rational search strategies in phase space, thus allowing for targeted further computational prediction and analysis of properties. The results presented here also constitute a useful guideline for synthesis of TMDs binary alloys via a range of synthesis techniques.
Efficient methods for one-shot quantum communication
Authors: Anshu Anurag , Jain Rahul 
Published: August 2022

AbstractWe address the question of efficient implementation of quantum protocols, with small communication and entanglement, and short depth circuit for encoding or decoding. We introduce two methods for this; the first constructs a resource-efficient convex-split lemma and the second adapts the technique of classical correlated sampling in computer science literature. These lead to the following consequences in one-shot quantum information theory. First concerns the task of quantum decoupling, achieved in many previous works with the aid of a random or pseudo-random unitary. We show that given any choice of basis such as the computational basis, decoupling can be achieved by a unitary that takes basis vectors to basis vectors. Thus, the circuit acts in a ‘classical’ manner; furthermore our unitary performs addition and multiplication modulo a prime. As the second consequence, we construct near-optimal communication protocol for quantum channel coding that uses exponentially smaller entanglement than the previous near-optimal protocol.
Natural switches in behaviour rapidly modulate hippocampal coding
Authors: Sarel Ayelet , Palgi Shaked , Blum Dan , Aljadeff Johnatan , Las Liora , Ulanovsky Nachum 
Published: August 2022

AbstractThroughout their daily lives, animals and humans often switch between different behaviours. However, neuroscience research typically studies the brain while the animal is performing one behavioural task at a time, and little is known about how brain circuits represent switches between different behaviours. Here we tested this question using an ethological setting: two bats flew together in a long 135 m tunnel, and switched between navigation when flying alone (solo) and collision avoidance as they flew past each other (cross-over). Bats increased their echolocation click rate before each cross-over, indicating attention to the other bat1–9. Hippocampal CA1 neurons represented the bat’s own position when flying alone (place coding10–14). Notably, during cross-overs, neurons switched rapidly to jointly represent the interbat distance by self-position. This neuronal switch was very fast—as fast as 100 ms—which could be revealed owing to the very rapid natural behavioural switch. The neuronal switch correlated with the attention signal, as indexed by echolocation. Interestingly, the different place fields of the same neuron often exhibited very different tuning to interbat distance, creating a complex non-separable coding of position by distance. Theoretical analysis showed that this complex representation yields more efficient coding. Overall, our results suggest that during dynamic natural behaviour, hippocampal neurons can rapidly switch their core computation to represent the relevant behavioural variables, supporting behavioural flexibility.
R-loop formation and conformational activation mechanisms of Cas9
Authors: Pacesa Martin , Loeff Luuk , Querques Irma , Muckenfuss Lena M. , Sawicka Marta , Jinek Martin 
Published: August 2022

AbstractCas9 is a CRISPR-associated endonuclease capable of RNA-guided, site-specific DNA cleavage1–3. The programmable activity of Cas9 has been widely utilized for genome editing applications4–6, yet its precise mechanisms of target DNA binding and off-target discrimination remain incompletely understood. Here we report a series of cryo-electron microscopy structures of Streptococcus pyogenes Cas9 capturing the directional process of target DNA hybridization. In the early phase of R-loop formation, the Cas9 REC2 and REC3 domains form a positively charged cleft that accommodates the distal end of the target DNA duplex. Guide–target hybridization past the seed region induces rearrangements of the REC2 and REC3 domains and relocation of the HNH nuclease domain to assume a catalytically incompetent checkpoint conformation. Completion of the guide–target heteroduplex triggers conformational activation of the HNH nuclease domain, enabled by distortion of the guide–target heteroduplex, and complementary REC2 and REC3 domain rearrangements. Together, these results establish a structural framework for target DNA-dependent activation of Cas9 that sheds light on its conformational checkpoint mechanism and may facilitate the development of novel Cas9 variants and guide RNA designs with enhanced specificity and activity.
Type I IFNs promote cancer cell stemness by triggering the epigenetic regulator KDM1B
Authors: Musella Martina , Guarracino Andrea , Manduca Nicoletta , Galassi Claudia , Ruggiero Eliana , Potenza Alessia , Maccafeo Ester , Manic Gwenola , Mattiello Luca , Soliman Abdel Rehim Sara , Signore Michele , Pietrosanto Marco , Helmer-Citterich Manuela , Pallocca Matteo , Fanciulli Maurizio , Bruno Tiziana , De Nicola Francesca , Corleone Giacomo , Di Benedetto Anna , Ercolani Cristiana , Pescarmona Edoardo , Pizzuti Laura , Guidi Francesco , Sperati Francesca , Vitale Sara , Macchia Daniele , Spada Massimo , Schiavoni Giovanna , Mattei Fabrizio , De Ninno Adele , Businaro Luca , Lucarini Valeria , Bracci Laura , Aricò Eleonora , Ziccheddu Giovanna , Facchiano Francesco , Rossi Stefania , Sanchez Massimo , Boe Alessandra , Biffoni Mauro , De Maria Ruggero , Vitale Ilio , Sistigu Antonella 
Published: August 2022

AbstractCancer stem cells (CSCs) are a subpopulation of cancer cells endowed with high tumorigenic, chemoresistant and metastatic potential. Nongenetic mechanisms of acquired resistance are increasingly being discovered, but molecular insights into the evolutionary process of CSCs are limited. Here, we show that type I interferons (IFNs-I) function as molecular hubs of resistance during immunogenic chemotherapy, triggering the epigenetic regulator demethylase 1B (KDM1B) to promote an adaptive, yet reversible, transcriptional rewiring of cancer cells towards stemness and immune escape. Accordingly, KDM1B inhibition prevents the appearance of IFN-I-induced CSCs, both in vitro and in vivo. Notably, IFN-I-induced CSCs are heterogeneous in terms of multidrug resistance, plasticity, invasiveness and immunogenicity. Moreover, in breast cancer (BC) patients receiving anthracycline-based chemotherapy, KDM1B positively correlated with CSC signatures. Our study identifies an IFN-I → KDM1B axis as a potent engine of cancer cell reprogramming, supporting KDM1B targeting as an attractive adjunctive to immunogenic drugs to prevent CSC expansion and increase the long-term benefit of therapy.
EPIC: Annotated epileptic EEG independent components for artifact reduction
Authors: Lopes Fábio , Leal Adriana , Medeiros Júlio , Pinto Mauro F. , Dourado António , Dümpelmann Matthias , Teixeira César 
Published: August 2022

AbstractScalp electroencephalogram is a non-invasive multi-channel biosignal that records the brain’s electrical activity. It is highly susceptible to noise that might overshadow important data. Independent component analysis is one of the most used artifact removal methods. Independent component analysis separates data into different components, although it can not automatically reject the noisy ones. Therefore, experts are needed to decide which components must be removed before reconstructing the data. To automate this method, researchers have developed classifiers to identify noisy components. However, to build these classifiers, they need annotated data. Manually classifying independent components is a time-consuming task. Furthermore, few labelled data are publicly available. This paper presents a source of annotated electroencephalogram independent components acquired from patients with epilepsy (EPIC Dataset). This dataset contains 77,426 independent components obtained from approximately 613 hours of electroencephalogram, visually inspected by two experts, which was already successfully utilised to develop independent component classifiers.