bluuebunny/crossref_metadata_2025_split huggingface dataset:
A potential explanation for the global increase in tropical cyclone rapid intensification
Authors: Bhatia Kieran , Baker Alexander , Yang Wenchang , Vecchi Gabriel , Knutson Thomas , Murakami Hiroyuki , Kossin James , Hodges Kevin , Dixon Keith , Bronselaer Benjamin , Whitlock Carolyn 
Published: November 2022

AbstractTropical cyclone rapid intensification events often cause destructive hurricane landfalls because they are associated with the strongest storms and forecasts with the highest errors. Multi-decade observational datasets of tropical cyclone behavior have recently enabled documentation of upward trends in tropical cyclone rapid intensification in several basins. However, a robust anthropogenic signal in global intensification trends and the physical drivers of intensification trends have yet to be identified. To address these knowledge gaps, here we compare the observed trends in intensification and tropical cyclone environmental parameters to simulated natural variability in a high-resolution global climate model. In multiple basins and the global dataset, we detect a significant increase in intensification rates with a positive contribution from anthropogenic forcing. Furthermore, thermodynamic environments around tropical cyclones have become more favorable for intensification, and climate models show anthropogenic warming has significantly increased the probability of these changes.
Non-Abelian anyon collider
Authors: Lee June-Young M. , Sim H.-S. 
Published: November 2022

AbstractA collider where particles are injected onto a beam splitter from opposite sides has been used for identifying quantum statistics of identical particles. The collision leads to bunching of the particles for bosons and antibunching for fermions. In recent experiments, a collider was applied to a fractional quantum Hall regime hosting Abelian anyons. The observed negative cross-correlation of electrical currents cannot be understood with fermionic antibunching. Here we predict, based on a conformal field theory and a non-perturbative treatment of non-equilibrium anyon injection, that the collider provides a tool for observation of the braiding statistics of various Abelian and non-Abelian anyons. Its dominant process is not direct collision between injected anyons, contrary to common expectation, but braiding between injected anyons and an anyon excited at the collider. The dependence of the resulting negative cross-correlation on the injection currents distinguishes non-Abelian SU(2)k anyons, Ising anyons, and Abelian Laughlin anyons.
Gate-tunable quantum pathways of high harmonic generation in graphene
Authors: Cha Soonyoung , Kim Minjeong , Kim Youngjae , Choi Shinyoung , Kang Sejong , Kim Hoon , Yoon Sangho , Moon Gunho , Kim Taeho , Lee Ye Won , Cho Gil Young , Park Moon Jeong , Kim Cheol-Joo , Kim B. J. , Lee JaeDong , Jo Moon-Ho , Kim Jonghwan 
Published: November 2022

AbstractUnder strong laser fields, electrons in solids radiate high-harmonic fields by travelling through quantum pathways in Bloch bands in the sub-laser-cycle timescales. Understanding these pathways in the momentum space through the high-harmonic radiation can enable an all-optical ultrafast probe to observe coherent lightwave-driven processes and measure electronic structures as recently demonstrated for semiconductors. However, such demonstration has been largely limited for semimetals because the absence of the bandgap hinders an experimental characterization of the exact pathways. In this study, by combining electrostatic control of chemical potentials with HHG measurement, we resolve quantum pathways of massless Dirac fermions in graphene under strong laser fields. Electrical modulation of HHG reveals quantum interference between the multi-photon interband excitation channels. As the light-matter interaction deviates beyond the perturbative regime, elliptically polarized laser fields efficiently drive massless Dirac fermions via an intricate coupling between the interband and intraband transitions, which is corroborated by our theoretical calculations. Our findings pave the way for strong-laser-field tomography of Dirac electrons in various quantum semimetals and their ultrafast electronics with a gate control.
Plastic bending in a semiconducting coordination polymer crystal enabled by delamination
Authors: An Lian-Cai , Li Xiang , Li Zhi-Gang , Li Qite , Beldon Patrick J. , Gao Fei-Fei , Li Zi-Ying , Zhu Shengli , Di Lu , Zhao Sanchuan , Zhu Jian , Comboni Davide , Kupenko Ilya , Li Wei , Ramamurty U. , Bu Xian-He 
Published: November 2022

AbstractCoordination polymers (CPs) are a class of crystalline solids that are considered brittle, due to the dominance of directional coordination bonding, which limits their utility in flexible electronics and wearable devices. Hence, engineering plasticity into functional CPs is of great importance. Here, we report plastic bending of a semiconducting CP crystal, Cu-Trz (Trz = 1,2,3-triazolate), that originates from delamination facilitated by the discrete bonding interactions along different crystallographic directions in the lattice. The coexistence of strong coordination bonds and weak supramolecular interactions, together with the unique molecular packing, are the structural features that enable the mechanical flexibility and anisotropic response. The spatially resolved analysis of short-range molecular forces reveals that the strong coordination bonds, and the adaptive C–H···π and Cu···Cu interactions, synergistically lead to the delamination of the local structures and consequently the associated mechanical bending. The proposed delamination mechanism offers a versatile tool for designing the plasticity of CPs and other molecular crystals.
Electronic photoreceptors enable prosthetic visual acuity matching the natural resolution in rats
Authors: Wang Bing-Yi , Chen Zhijie Charles , Bhuckory Mohajeet , Huang Tiffany , Shin Andrew , Zuckerman Valentina , Ho Elton , Rosenfeld Ethan , Galambos Ludwig , Kamins Theodore , Mathieson Keith , Palanker Daniel 
Published: November 2022

AbstractLocalized stimulation of the inner retinal neurons for high-acuity prosthetic vision requires small pixels and minimal crosstalk from the neighboring electrodes. Local return electrodes within each pixel limit the crosstalk, but they over-constrain the electric field, thus precluding the efficient stimulation with subretinal pixels smaller than 55 μm. Here we demonstrate a high-resolution prosthetic vision based on a novel design of a photovoltaic array, where field confinement is achieved dynamically, leveraging the adjustable conductivity of the diodes under forward bias to turn the designated pixels into transient returns. We validated the computational modeling of the field confinement in such an optically-controlled circuit by in-vitro and in-vivo measurements. Most importantly, using this strategy, we demonstrated that the grating acuity with 40 μm pixels matches the pixel pitch, while with 20 μm pixels, it reaches the 28 μm limit of the natural visual resolution in rats. This method enables customized field shaping based on individual retinal thickness and distance from the implant, paving the way to higher acuity of prosthetic vision in atrophic macular degeneration.
Lamin A/C-dependent chromatin architecture safeguards naïve pluripotency to prevent aberrant cardiovascular cell fate and function
Authors: Wang Yinuo , Elsherbiny Adel , Kessler Linda , Cordero Julio , Shi Haojie , Serke Heike , Lityagina Olga , Trogisch Felix A. , Mohammadi Mona Malek , El-Battrawy Ibrahim , Backs Johannes , Wieland Thomas , Heineke Joerg , Dobreva Gergana 
Published: November 2022

AbstractTight control of cell fate choices is crucial for normal development. Here we show that lamin A/C plays a key role in chromatin organization in embryonic stem cells (ESCs), which safeguards naïve pluripotency and ensures proper cell fate choices during cardiogenesis. We report changes in chromatin compaction and localization of cardiac genes in Lmna−/− ESCs resulting in precocious activation of a transcriptional program promoting cardiomyocyte versus endothelial cell fate. This is accompanied by premature cardiomyocyte differentiation, cell cycle withdrawal and abnormal contractility. Gata4 is activated by lamin A/C loss and Gata4 silencing or haploinsufficiency rescues the aberrant cardiovascular cell fate choices induced by lamin A/C deficiency. We uncover divergent functions of lamin A/C in naïve pluripotent stem cells and cardiomyocytes, which have distinct contributions to the transcriptional alterations of patients with LMNA-associated cardiomyopathy. We conclude that disruption of lamin A/C-dependent chromatin architecture in ESCs is a primary event in LMNA loss-of-function cardiomyopathy.
VeChat: correcting errors in long reads using variation graphs
Authors: Luo Xiao , Kang Xiongbin , Schönhuth Alexander 
Published: November 2022

AbstractError correction is the canonical first step in long-read sequencing data analysis. Current self-correction methods, however, are affected by consensus sequence induced biases that mask true variants in haplotypes of lower frequency showing in mixed samples. Unlike consensus sequence templates, graph-based reference systems are not affected by such biases, so do not mistakenly mask true variants as errors. We present VeChat, as an approach to implement this idea: VeChat is based on variation graphs, as a popular type of data structure for pangenome reference systems. Extensive benchmarking experiments demonstrate that long reads corrected by VeChat contain 4 to 15 (Pacific Biosciences) and 1 to 10 times (Oxford Nanopore Technologies) less errors than when being corrected by state of the art approaches. Further, using VeChat prior to long-read assembly significantly improves the haplotype awareness of the assemblies. VeChat is an easy-to-use open-source tool and publicly available athttps://github.com/HaploKit/vechat.
Pan-cancer single-cell analysis reveals the heterogeneity and plasticity of cancer-associated fibroblasts in the tumor microenvironment
Authors: Luo Han , Xia Xuyang , Huang Li-Bin , An Hyunsu , Cao Minyuan , Kim Gyeong Dae , Chen Hai-Ning , Zhang Wei-Han , Shu Yang , Kong Xiangyu , Ren Zhixiang , Li Pei-Heng , Liu Yang , Tang Huairong , Sun Ronghao , Li Chao , Bai Bing , Jia Weiguo , Liu Yi , Zhang Wei , Yang Li , Peng Yong , Dai Lunzhi , Hu Hongbo , Jiang Yong , Hu Yiguo , Zhu Jingqiang , Jiang Hong , Li Zhihui , Caulin Carlos , Park Jihwan , Xu Heng 
Published: November 2022

AbstractCancer-associated fibroblasts (CAFs) are the predominant components of the tumor microenvironment (TME) and influence cancer hallmarks, but without systematic investigation on their ubiquitous characteristics across different cancer types. Here, we perform pan-cancer analysis on 226 samples across 10 solid cancer types to profile the TME at single-cell resolution, illustrating the commonalities/plasticity of heterogenous CAFs. Activation trajectory of the major CAF types is divided into three states, exhibiting distinct interactions with other cell components, and relating to prognosis of immunotherapy. Moreover, minor CAF components represent the alternative origin from other TME components (e.g., endothelia and macrophages). Particularly, the ubiquitous presentation of endothelial-to-mesenchymal transition CAF, which may interact with proximal SPP1+ tumor-associated macrophages, is implicated in endothelial-to-mesenchymal transition and survival stratifications. Our study comprehensively profiles the shared characteristics and dynamics of CAFs, and highlight their heterogeneity and plasticity across different cancer types. Browser of integrated pan-cancer single-cell information is available at https://gist-fgl.github.io/sc-caf-atlas/.
Modular total syntheses of trans-clerodanes and sesquiterpene (hydro)quinones via tail-to-head cyclization and reductive coupling strategies
Authors: Zhu Wenming , Yin Qishuang , Lou Zhizheng , Yang Ming 
Published: November 2022

AbstractThetrans-clerodanes and sesquiterpene (hydro)quinones are a growing class of natural products that exhibit a wide range of biological activities. Although they are different types of natural products, some of them feature the sametrans-decalin core structure. Here, we report the total syntheses of two members oftrans-clerodanes, five members of sesquiterpene (hydro)quinones as well as the proposed structure of dysidavarone D via a modular synthetic route. A bioinspired tail-to-head cyclization strategy was developed to syntheses of thetrans-decalin architectures by using two diastereochemically complementary radical polyene cyclization reactions catalyzed by Ti(III) and mediated by Mn(III), respectively. The different types of side chains were introduced by challenging nickel catalyzed reductive couplings of sterically hindered alkyl halides. The synthesis of the proposed dysidavarone D proved a wrong structural assignment of the natural product.
Translation regulatory factor BZW1 regulates preimplantation embryo development and compaction by restricting global non-AUG Initiation
Authors: Zhang Jue , Pi Shuai-Bo , Zhang Nan , Guo Jing , Zheng Wei , Leng Lizhi , Lin Ge , Fan Heng-Yu 
Published: November 2022

AbstractProtein synthesis is an essential step in gene expression during the development of mammalian preimplantation embryos. This is a complex and highly regulated process. The accuracy of the translation initiation codon is important in various gene expression programs. However, the mechanisms that regulate AUG and non-AUG codon initiation in early embryos remain poorly understood. BZW1 is a key factor in determining the mRNA translation start codon. Here, we show that BZW1 is essential for early embryonic development in mice. Bzw1-knockdown embryos fail to undergo compaction, and show decreased blastocyst formation rates. We also observe defects in the differentiation capacity and implantation potential after Bzw1 interference. Further investigation revealed that Bzw1 knockdown causes the levels of translation initiation with CUG as the start codon to increase. The decline in BZW1 levels result in a decrease in protein synthesis in preimplantation embryos, whereas the total mRNA levels are not altered. Therefore, we concluded that BZW1 contributes to protein synthesis during early embryonic development by restricting non-AUG translational initiation.
2′–5′ oligoadenylate synthetase‑like 1 (OASL1) protects against atherosclerosis by maintaining endothelial nitric oxide synthase mRNA stability
Authors: Kim Tae Kyeong , Jeon Sejin , Park Seonjun , Sonn Seong-Keun , Seo Seungwoon , Suh Joowon , Jin Jing , Kweon Hyae Yon , Kim Sinai , Moon Shin Hye , Kweon Okhee , Koo Bon-Hyeock , Kim Nayoung , Lee Hae-Ock , Kim Young-Myeong , Kim Young-Joon , Park Sung Ho , Oh Goo Taeg 
Published: November 2022

AbstractEndothelial nitric oxide synthase (eNOS) decreases following inflammatory stimulation. As a master regulator of endothelial homeostasis, maintaining optimal eNOS levels is important during cardiovascular events. However, little is known regarding the mechanism of eNOS protection. In this study, we demonstrate a regulatory role for endothelial expression of 2′–5′ oligoadenylate synthetase-like 1 (OASL1) in maintaining eNOS mRNA stability during athero-prone conditions and consider its clinical implications. A lack of endothelial Oasl1 accelerated plaque progression, which was preceded by endothelial dysfunction, elevated vascular inflammation, and decreased NO bioavailability following impaired eNOS expression. Mechanistically, knockdown of PI3K/Akt signaling-dependent OASL expression increased Erk1/2 and NF-κB activation and decreased NOS3 (gene name for eNOS) mRNA expression through upregulation of the negative regulatory, miR-584, whereas a miR-584 inhibitor rescued the effects of OASL knockdown. These results suggest that OASL1/OASL regulates endothelial biology by protecting NOS3 mRNA and targeting miR-584 represents a rational therapeutic strategy for eNOS maintenance in vascular disease.
Updated vaccine protects against SARS-CoV-2 variants including Omicron (B.1.1.529) and prevents transmission in hamsters
Authors: Sharma Sapna , Vercruysse Thomas , Sanchez-Felipe Lorena , Kerstens Winnie , Rasulova Madina , Bervoets Lindsey , De Keyzer Carolien , Abdelnabi Rana , Foo Caroline S. , Lemmens Viktor , Van Looveren Dominique , Maes Piet , Baele Guy , Weynand Birgit , Lemey Philippe , Neyts Johan , Thibaut Hendrik Jan , Dallmeier Kai 
Published: November 2022

AbstractCurrent COVID-19 vaccines are based on prototypic spike sequences from ancestral 2019 SARS-CoV-2 strains. However, the ongoing pandemic is fueled by variants of concern (VOC) escaping vaccine-mediated protection. Here we demonstrate how immunization in hamsters using prototypic spike expressed from yellow fever 17D (YF17D) as vector blocks ancestral virus (B lineage) and VOC Alpha (B.1.1.7) yet fails to fully protect from Beta (B.1.351). However, the same YF17D vectored vaccine candidate with an evolved antigen induced considerably improved neutralizing antibody responses against VOCs Beta, Gamma (P.1) and the recently predominant Omicron (B.1.1.529), while maintaining immunogenicity against ancestral virus and VOC Delta (B.1.617.2). Thus vaccinated animals resisted challenge by all VOCs, including vigorous high titre exposure to the most difficult to cover Beta, Delta and Omicron variants, eliminating detectable virus and markedly improving lung pathology. Finally, vaccinated hamsters did not transmit Delta variant to non-vaccinated cage mates. Overall, our data illustrate how current first-generation COVID-19 vaccines may need to be updated to maintain efficacy against emerging VOCs and their spread at community level.
Identification of evolutionarily conserved regulators of muscle mitochondrial network organization
Authors: Katti Prasanna , Ajayi Peter T. , Aponte Angel , Bleck Christopher K. E. , Glancy Brian 
Published: November 2022

AbstractMitochondrial networks provide coordinated energy distribution throughout muscle cells. However, pathways specifying mitochondrial networks are incompletely understood and it is unclear how they might affect contractile fiber-type. Here, we show that natural energetic demands placed on Drosophila melanogaster muscles yield native cell-types among which contractile and mitochondrial network-types are regulated differentially. Proteomic analyses of indirect flight, jump, and leg muscles, together with muscles misexpressing known fiber-type specification factor salm, identified transcription factors H15 and cut as potential mitochondrial network regulators. We demonstrate H15 operates downstream of salm regulating flight muscle contractile and mitochondrial network-type. Conversely, H15 regulates mitochondrial network configuration but not contractile type in jump and leg muscles. Further, we find that cut regulates salm expression in flight muscles and mitochondrial network configuration in leg muscles. These data indicate cell type-specific regulation of muscle mitochondrial network organization through evolutionarily conserved transcription factors cut, salm, and H15.
Base-editing-mediated dissection of a γ-globin cis-regulatory element for the therapeutic reactivation of fetal hemoglobin expression
Authors: Antoniou Panagiotis , Hardouin Giulia , Martinucci Pierre , Frati Giacomo , Felix Tristan , Chalumeau Anne , Fontana Letizia , Martin Jeanne , Masson Cecile , Brusson Megane , Maule Giulia , Rosello Marion , Giovannangeli Carine , Abramowski Vincent , de Villartay Jean-Pierre , Concordet Jean-Paul , Del Bene Filippo , El Nemer Wassim , Amendola Mario , Cavazzana Marina , Cereseto Anna , Romano Oriana , Miccio Annarita 
Published: November 2022

AbstractSickle cell disease and β-thalassemia affect the production of the adult β-hemoglobin chain. The clinical severity is lessened by mutations that cause fetal γ-globin expression in adult life (i.e., the hereditary persistence of fetal hemoglobin). Mutations clustering ~200 nucleotides upstream of the HBG transcriptional start sites either reduce binding of the LRF repressor or recruit the KLF1 activator. Here, we use base editing to generate a variety of mutations in the −200 region of the HBG promoters, including potent combinations of four to eight γ-globin-inducing mutations. Editing of patient hematopoietic stem/progenitor cells is safe, leads to fetal hemoglobin reactivation and rescues the pathological phenotype. Creation of a KLF1 activator binding site is the most potent strategy – even in long-term repopulating hematopoietic stem/progenitor cells. Compared with a Cas9-nuclease approach, base editing avoids the generation of insertions, deletions and large genomic rearrangements and results in higher γ-globin levels. Our results demonstrate that base editing of HBG promoters is a safe, universal strategy for treating β-hemoglobinopathies.
Metabolite annotation from knowns to unknowns through knowledge-guided multi-layer metabolic networking
Authors: Zhou Zhiwei , Luo Mingdu , Zhang Haosong , Yin Yandong , Cai Yuping , Zhu Zheng-Jiang 
Published: November 2022

AbstractLiquid chromatography - mass spectrometry (LC-MS) based untargeted metabolomics allows to measure both known and unknown metabolites in the metabolome. However, unknown metabolite annotation is a major challenge in untargeted metabolomics. Here, we develop an approach, namely, knowledge-guided multi-layer network (KGMN), to enable global metabolite annotation from knowns to unknowns in untargeted metabolomics. The KGMN approach integrates three-layer networks, including knowledge-based metabolic reaction network, knowledge-guided MS/MS similarity network, and global peak correlation network. To demonstrate the principle, we apply KGMN in an in vitro enzymatic reaction system and different biological samples, with ~100–300 putative unknowns annotated in each data set. Among them, >80% unknown metabolites are corroborated with in silico MS/MS tools. Finally, we validate 5 metabolites that are absent in common MS/MS libraries through repository mining and synthesis of chemical standards. Together, the KGMN approach enables efficient unknown annotations, and substantially advances the discovery of recurrent unknown metabolites for common biological samples from model organisms, towards deciphering dark matter in untargeted metabolomics.
Hyperbolic material enhanced scattering nanoscopy for label-free super-resolution imaging
Authors: Lee Yeon Ui , Li Shilong , Wisna G. Bimananda M. , Zhao Junxiang , Zeng Yuan , Tao Andrea R. , Liu Zhaowei 
Published: November 2022

AbstractFluorescence super-resolution microscopy has, over the last two decades, been extensively developed to access deep-subwavelength nanoscales optically. Label-free super-resolution technologies however have only achieved a slight improvement compared to the diffraction limit. In this context, we demonstrate a label-free imaging method, i.e., hyperbolic material enhanced scattering (HMES) nanoscopy, which breaks the diffraction limit by tailoring the light-matter interaction between the specimens and a hyperbolic material substrate. By exciting the highly confined evanescent hyperbolic polariton modes with dark-field detection, HMES nanoscopy successfully shows a high-contrast scattering image with a spatial resolution around 80 nm. Considering the wavelength at 532 nm and detection optics with a 0.6 numerical aperture (NA) objective lens, this value represents a 5.5-fold resolution improvement beyond the diffraction limit. HMES provides capabilities for super-resolution imaging where fluorescence is not available or challenging to apply.