bluuebunny/crossref_metadata_2025_split huggingface dataset:
SMG6 regulates DNA damage and cell survival in Hippo pathway kinase LATS2-inactivated malignant mesothelioma
Authors: Suzuki Koya , Tange Masaki , Yamagishi Ryota , Hanada Hiroyuki , Mukai Satomi , Sato Tatsuhiro , Tanaka Takeshi , Akashi Tomohiro , Kadomatsu Kenji , Maeda Tohru , Miida Takashi , Takeuchi Ichiro , Murakami Hiroshi , Sekido Yoshitaka , Murakami-Tonami Yuko 
Published: November 2022

AbstractMany genes responsible for Malignant mesothelioma (MM) have been identified as tumor suppressor genes and it is difficult to target these genes directly at a molecular level. We searched for the gene which showed synthetic lethal phenotype with LATS2, one of the MM causative genes and one of the kinases in the Hippo pathway. Here we showed that knockdown of SMG6 results in synthetic lethality in LATS2-inactivated cells. We found that this synthetic lethality required the nuclear translocation of YAP1 and TAZ. Both are downstream factors of the Hippo pathway. We also demonstrated that this synthetic lethality did not require SMG6 in nonsense-mediated mRNA decay (NMD) but in regulating telomerase reverse transcriptase (TERT) activity. In addition, the RNA-dependent DNA polymerase (RdDP) activity of TERT was required for this synthetic lethal phenotype. We confirmed the inhibitory effects of LATS2 and SMG6 on cell proliferation in vivo. The result suggests an interaction between the Hippo and TERT signaling pathways. We also propose that SMG6 and TERT are novel molecular target candidates for LATS2-inactivated cancers such as MM.
Structure insights into selective coupling of G protein subtypes by a class B G protein-coupled receptor
Authors: Zhao Li-Hua , Lin Jingyu , Ji Su-Yu , Zhou X. Edward , Mao Chunyou , Shen Dan-Dan , He Xinheng , Xiao Peng , Sun Jinpeng , Melcher Karsten , Zhang Yan , Yu Xiao , Xu H. Eric 
Published: November 2022

AbstractThe ability to couple with multiple G protein subtypes, such as Gs, Gi/o, or Gq/11, by a given G protein-coupled receptor (GPCR) is critical for many physiological processes. Over the past few years, the cryo-EM structures for all 15 members of the medically important class B GPCRs, all in complex with Gs protein, have been determined. However, no structure of class B GPCRs with Gq/11 has been solved to date, limiting our understanding of the precise mechanisms of G protein coupling selectivity. Here we report the structures of corticotropin releasing factor receptor 2 (CRF2R) bound to Urocortin 1 (UCN1), coupled with different classes of heterotrimeric G proteins, G11 and Go. We compare these structures with the structure of CRF2R in complex with Gs to uncover the structural differences that determine the selective coupling of G protein subtypes by CRF2R. These results provide important insights into the structural basis for the ability of CRF2R to couple with multiple G protein subtypes.
Hi-TrAC reveals division of labor of transcription factors in organizing chromatin loops
Authors: Liu Shuai , Cao Yaqiang , Cui Kairong , Tang Qingsong , Zhao Keji 
Published: November 2022

AbstractThe three-dimensional genomic structure plays a critical role in gene expression, cellular differentiation, and pathological conditions. It is pivotal to elucidate fine-scale chromatin architectures, especially interactions of regulatory elements, to understand the temporospatial regulation of gene expression. In this study, we report Hi-TrAC as a proximity ligation-free, robust, and sensitive technique to profile genome-wide chromatin interactions at high-resolution among regulatory elements. Hi-TrAC detects chromatin looping among accessible regions at single nucleosome resolution. With almost half-million identified loops, we reveal a comprehensive interaction network of regulatory elements across the genome. After integrating chromatin binding profiles of transcription factors, we discover that cohesin complex and CTCF are responsible for organizing long-range chromatin loops, related to domain formation; whereas ZNF143 and HCFC1 are involved in structuring short-range chromatin loops between regulatory elements, which directly regulate gene expression. Thus, we introduce a methodology to identify a delicate and comprehensive network of cis-regulatory elements, revealing the complexity and a division of labor of transcription factors in organizing chromatin loops for genome organization and gene expression.
Anisotropic dislocation-domain wall interactions in ferroelectrics
Authors: Zhuo Fangping , Zhou Xiandong , Gao Shuang , Höfling Marion , Dietrich Felix , Groszewicz Pedro B. , Fulanović Lovro , Breckner Patrick , Wohninsland Andreas , Xu Bai-Xiang , Kleebe Hans-Joachim , Tan Xiaoli , Koruza Jurij , Damjanovic Dragan , Rödel Jürgen 
Published: November 2022

AbstractDislocations are usually expected to degrade electrical, thermal and optical functionality and to tune mechanical properties of materials. Here, we demonstrate a general framework for the control of dislocation–domain wall interactions in ferroics, employing an imprinted dislocation network. Anisotropic dielectric and electromechanical properties are engineered in barium titanate crystals via well-controlled line-plane relationships, culminating in extraordinary and stable large-signal dielectric permittivity (≈23100) and piezoelectric coefficient (≈2470 pm V–1). In contrast, a related increase in properties utilizing point-plane relation prompts a dramatic cyclic degradation. Observed dielectric and piezoelectric properties are rationalized using transmission electron microscopy and time- and cycle-dependent nuclear magnetic resonance paired with X-ray diffraction. Succinct mechanistic understanding is provided by phase-field simulations and driving force calculations of the described dislocation–domain wall interactions. Our 1D-2D defect approach offers a fertile ground for tailoring functionality in a wide range of functional material systems.
Diffusion MRI anisotropy in the cerebral cortex is determined by unmyelinated tissue features
Authors: Reveley Colin , Ye Frank Q. , Mars Rogier B. , Matrov Denis , Chudasama Yogita , Leopold David A. 
Published: November 2022

AbstractDiffusion magnetic resonance imaging (dMRI) is commonly used to assess the tissue and cellular substructure of the human brain. In the white matter, myelinated axons are the principal neural elements that shape dMRI through the restriction of water diffusion; however, in the gray matter the relative contributions of myelinated axons and other tissue features to dMRI are poorly understood. Here we investigate the determinants of diffusion in the cerebral cortex. Specifically, we ask whether myelinated axons significantly shape dMRI fractional anisotropy (dMRI-FA), a measure commonly used to characterize tissue properties in humans. We compared ultra-high resolution ex vivo dMRI data from the brain of a marmoset monkey with both myelin- and Nissl-stained histological sections obtained from the same brain after scanning. We found that the dMRI-FA did not match the spatial distribution of myelin in the gray matter. Instead dMRI-FA was more closely related to the anisotropy of stained tissue features, most prominently those revealed by Nissl staining and to a lesser extent those revealed by myelin staining. Our results suggest that unmyelinated neurites such as large caliber apical dendrites are the primary features shaping dMRI measures in the cerebral cortex.
A biomimetic electrostatic assistance for guiding and promoting N-terminal protein chemical modification
Authors: Ollivier Nathalie , Sénéchal Magalie , Desmet Rémi , Snella Benoît , Agouridas Vangelis , Melnyk Oleg 
Published: November 2022

AbstractThe modification of protein electrostatics by phosphorylation is a mechanism used by cells to promote the association of proteins with other biomolecules. In this work, we show that introducing negatively charged phosphoserines in a reactant is a powerful means for directing and accelerating the chemical modification of proteins equipped with oppositely charged arginines. While the extra charged amino acid residues induce no detectable affinity between the reactants, they bring site-selectivity to a reaction that is otherwise devoid of such a property. They also enable rate accelerations of four orders of magnitude in some cases, thereby permitting chemical processes to proceed at the protein level in the low micromolar range, using reactions that are normally too slow to be useful in such dilute conditions.
Anomalous universal conductance as a hallmark of non-locality in a Majorana-hosted superconducting island
Authors: Hao Yiru , Zhang Gu , Liu Donghao , Liu Dong E. 
Published: November 2022

AbstractThe non-local feature of topological states of matter is the key for the topological protection of quantum information and enables robust non-local manipulation in quantum information. Here we propose to manifest the non-local feature of a Majorana-hosted superconducting island by measuring the temperature dependence of Coulomb blockade peak conductance in different regimes. In the low-temperature regime, we discover a coherent double Majorana-assisted teleportation (MT) process, where any independent tunneling process always involves two coherent non-local MTs; and we also find an anomalous universal scaling behavior, i.e., a crossover from a $${[\max (T,eV)]}^{6}$$

[

max

(

T
,
e
V

)

]

6

power-law to a $${[\max (T,eV)]}^{3}$$

[

max

(

T
,
e
V

)

]

3

power-law conductance behavior when energy scale increases — in stark contrast to the usual exponential suppression due to certain local transport. In the high-temperature regime, the conductance is instead proportional to the temperature inverse, indicating a non-monotonic temperature-dependence of the conductance. Both the anomalous power law and non-monotonic temperature-dependence of the conductance can be distinguished from the conductance peak in the traditional Coulomb block, and therefore, together serve as a hallmark for the non-local feature in the Majorana-hosted superconducting island.
Stokes meta-hologram toward optical cryptography
Authors: Guo Xuyue , Li Peng , Zhong Jinzhan , Wen Dandan , Wei Bingyan , Liu Sheng , Qi Shuxia , Zhao Jianlin 
Published: November 2022

AbstractOptical cryptography manifests itself a powerful platform for information security, which involves encrypting secret images into visual patterns. Recently, encryption schemes demonstrated on metasurface platform have revolutionized optical cryptography, as the versatile design concept allows for unrestrained creativity. Despite rapid progresses, most efforts focus on the functionalities of cryptography rather than addressing performance issues, such as deep security, information capacity, and reconstruction quality. Here, we develop an optical encryption scheme by integrating visual cryptography with metasurface-assisted pattern masking, referred to as Stokes meta-hologram. Based on spatially structured polarization pattern masking, Stokes meta-hologram allows multichannel vectorial encryption to mask multiple secret images into unrecognizable visual patterns, and retrieve them following Stokes vector analysis. Further, an asymmetric encryption scheme based on Stokes vector rotation transformation is proposed to settle the inherent problem of the need to share the key in symmetric encryption. Our results show that Stokes meta-hologram can achieve optical cryptography with effectively improved security, and thereby paves a promising pathway toward optical and quantum security, optical communications, and anticounterfeiting.
Ultrasensitive probing of plasmonic hot electron occupancies
Authors: Budai Judit , Pápa Zsuzsanna , Petrik Péter , Dombi Péter 
Published: November 2022

AbstractNon-thermal and thermal carrier populations in plasmonic systems raised significant interest in contemporary fundamental and applied physics. Although the theoretical description predicts not only the energies but also the location of the generated carriers, the experimental justification of these theories is still lacking. Here, we demonstrate experimentally that upon the optical excitation of surface plasmon polaritons, a non-thermal electron population appears in the topmost domain of the plasmonic film directly coupled to the local fields. The applied all-optical method is based on spectroscopic ellipsometric determination of the dielectric function, allowing us to obtain in-depth information on surface plasmon induced changes of the directly related electron occupancies. The ultrahigh sensitivity of our method allows us to capture the signatures of changes induced by electron-electron scattering processes with ultrafast decay times. These experiments shed light on the build-up of plasmonic hot electron population in nanoscale media.
RNA-binding proteins of KHDRBS and IGF2BP families control the oncogenic activity of MLL-AF4
Authors: Okuda Hiroshi , Miyamoto Ryo , Takahashi Satoshi , Kawamura Takeshi , Ichikawa Juri , Harada Ibuki , Tamura Tomohiko , Yokoyama Akihiko 
Published: November 2022

AbstractChromosomal translocation generates the MLL-AF4 fusion gene, which causes acute leukemia of multiple lineages. MLL-AF4 is a strong oncogenic driver that induces leukemia without additional mutations and is the most common cause of pediatric leukemia. However, establishment of a murine disease model via retroviral transduction has been difficult owning to a lack of understanding of its regulatory mechanisms. Here, we show that MLL-AF4 protein is post-transcriptionally regulated by RNA-binding proteins, including those of KHDRBS and IGF2BP families. MLL-AF4 translation is inhibited by ribosomal stalling, which occurs at regulatory sites containing AU-rich sequences recognized by KHDRBSs. Synonymous mutations disrupting the association of KHDRBSs result in proper translation of MLL-AF4 and leukemic transformation. Consequently, the synonymous MLL-AF4 mutant induces leukemia in vivo. Our results reveal that post-transcriptional regulation critically controls the oncogenic activity of MLL-AF4; these findings might be valuable in developing novel therapies via modulation of the activity of RNA-binding proteins.
Autoinducer-2 and bile salts induce c-di-GMP synthesis to repress the T3SS via a T3SS chaperone
Authors: Li Shuyu , Sun Hengxi , Li Jianghan , Zhao Yujiao , Wang Ruiying , Xu Lei , Duan Chongyi , Li Jialin , Wang Zhuo , Liu Qinmeng , Wang Yao , Ouyang Songying , Shen Xihui , Zhang Lei 
Published: November 2022

AbstractCyclic di-GMP (c-di-GMP) transduces extracellular stimuli into intracellular responses, coordinating a plethora of important biological processes. Low levels of c-di-GMP are often associated with highly virulent behavior that depends on the type III secretion system (T3SS) effectors encoded, whereas elevated levels of c-di-GMP lead to the repression of T3SSs. However, extracellular signals that modulate c-di-GMP metabolism to control T3SSs and c-di-GMP effectors that relay environmental stimuli to changes in T3SS activity remain largely obscure. Here, we show that the quorum sensing signal autoinducer-2 (AI-2) induces c-di-GMP synthesis via a GAPES1 domain-containing diguanylate cyclase (DGC) YeaJ to repress T3SS-1 gene expression inSalmonella entericaserovar Typhimurium. YeaJ homologs capable of sensing AI-2 are present in many other species belonging toEnterobacterales. We also reveal that taurocholate and taurodeoxycholate bind to the sensory domain of the DGC YedQ to induce intracellular accumulation of c-di-GMP, thus repressing the expression of T3SS-1 genes. Further, we find that c-di-GMP negatively controls the function of T3SSs through binding to the widely conserved CesD/SycD/LcrH family of T3SS chaperones. Our results support a model in which bacteria sense changes in population density and host-derived cues to regulate c-di-GMP synthesis, thereby modulating the activity of T3SSs via a c-di-GMP-responsive T3SS chaperone.
Granular piston-probing in microgravity: powder compression, from densification to jamming
Authors: D’Angelo Olfa , Horb Anabelle , Cowley Aidan , Sperl Matthias , Kranz W. Till 
Published: November 2022

AbstractThe macroscopic response of granular solids is determined by the microscopic fabric of force chains, which, in turn, is intimately linked to the history of the solid. To query the influence of gravity on powder flow behavior, a granular material is subjected to compression by a piston in a closed container, on-ground and in microgravity (on parabolic flights). Results show that piston-probing densifies the packing, eventually leading to jamming of the material compressed by the piston, regardless of the gravitational environment. The onset of jamming is found to appear at lower packing fraction in microgravity ($${\varphi }_{J}^{\mu -{{{\rm{g}}}}}=0.567\pm 0.014$$

φ

J

μ
−
g

=
0.567
±
0.014

) than on-ground ($${\varphi }_{J}^{{{{\rm{gnd}}}}}=0.579\pm 0.014$$

φ

J

gnd

=
0.579
±
0.014

). We interpret these findings as the manifestation of a granular fabric altered by the gravitational force field: in absence of a secondary load (due to gravitational acceleration) to stimulate reorganization in a different direction to the major compression stress, the particles’ configuration becomes stable at lower density, as the particles have no external drive to promote reorganization into a denser packing. This is coupled with a change in interparticular force balance which takes place under low gravity, as cohesive interactions become predominant. We propose a combination of microscopic and continuum arguments to rationalize our results.
Pre- and post-surgery brain tumor multimodal magnetic resonance imaging data optimized for large scale computational modelling
Authors: Aerts Hannelore , Colenbier Nigel , Almgren Hannes , Dhollander Thijs , Daparte Javier Rasero , Clauw Kenzo , Johri Amogh , Meier Jil , Palmer Jessica , Schirner Michael , Ritter Petra , Marinazzo Daniele 
Published: November 2022

AbstractWe present a dataset of magnetic resonance imaging (MRI) data (T1, diffusion, BOLD) acquired in 25 brain tumor patients before the tumor resection surgery, and six months after the surgery, together with the tumor masks, and in 11 controls (recruited among the patients’ caregivers). The dataset also contains behavioral and emotional scores obtained with standardized questionnaires. To simulate personalized computational models of the brain, we also provide structural connectivity matrices, necessary to perform whole-brain modelling with tools such as The Virtual Brain. In addition, we provide blood-oxygen-level-dependent imaging time series averaged across regions of interest for comparison with simulation results. An average resting state hemodynamic response function for each region of interest, as well as shape maps for each voxel, are also contributed.
Incidence, risk factors and prognosis of acute kidney injury in patients treated with immune checkpoint inhibitors: a retrospective study
Authors: Ji Ming-Su , Wu Rilige , Feng Zhe , Wang Yuan-Da , Wang Yong , Zhang Li , Sun Xue-Feng , Chen Xiang-Mei , He Kun-Lun , Cai Guang-Yan 
Published: November 2022

AbstractImmune checkpoint inhibitors (ICIs) change the prognosis of many cancer patients. With the increasing use of ICIs, immune-related adverse events are occurring, including acute kidney injury (AKI). This study aimed to assess the incidence of AKI during ICI treatment and its risk factors and impact on mortality. Patients treated with ICIs at the First Medical Center of the Chinese PLA General Hospital from January 1, 2014, to December 30, 2019, were consecutively enrolled, and risk factors affecting AKI development in patients treated with ICIs were analyzed using univariate and multivariate logistic regression. Medical record surveys and telephone inquiry were used for follow-up, and Kaplan–Meier survival analysis and Cox regression were used to analyze independent risk factors for death. Among 1615 patients, 114 (7.1%) had AKI. Multivariate logistic regression analysis showed that anemia, Alb < 30 g/L, antibiotic use, diuretic use, NSAID use and proton pump inhibitor use were independent risk factors for AKI development in patients treated with ICIs. Stage 2 or 3 AKI was an independent risk factor for nonrecovery of renal function after AKI onset. Multivariate Cox regression analysis showed that anemia, Alb < 30 g/L, AKI occurrence, and diuretic use were independent risk factors for death in patients treated with ICIs, while high baseline BMI, other tumor types, ACEI/ARB use, and chemotherapy use were protective factors for patient death. AKI occurs in 7.1% of patients treated with ICIs. Anemia, Alb < 30 g/L, and combined medication use are independent risk factors for AKI in patients treated with ICIs. Anemia, Alb < 30 g/L, AKI occurrence, and diuretic use were independent risk factors for death in patients treated with ICIs.
Brain activity during shadowing of audiovisual cocktail party speech, contributions of auditory–motor integration and selective attention
Authors: Wikman Patrik , Ylinen Artturi , Leminen Miika , Alho Kimmo 
Published: November 2022

AbstractSelective listening to cocktail-party speech involves a network of auditory and inferior frontal cortical regions. However, cognitive and motor cortical regions are differentially activated depending on whether the task emphasizes semantic or phonological aspects of speech. Here we tested whether processing of cocktail-party speech differs when participants perform a shadowing (immediate speech repetition) task compared to an attentive listening task in the presence of irrelevant speech. Participants viewed audiovisual dialogues with concurrent distracting speech during functional imaging. Participants either attentively listened to the dialogue, overtly repeated (i.e., shadowed) attended speech, or performed visual or speech motor control tasks where they did not attend to speech and responses were not related to the speech input. Dialogues were presented with good or poor auditory and visual quality. As a novel result, we show that attentive processing of speech activated the same network of sensory and frontal regions during listening and shadowing. However, in the superior temporal gyrus (STG), peak activations during shadowing were posterior to those during listening, suggesting that an anterior–posterior distinction is present for motor vs. perceptual processing of speech already at the level of the auditory cortex. We also found that activations along the dorsal auditory processing stream were specifically associated with the shadowing task. These activations are likely to be due to complex interactions between perceptual, attention dependent speech processing and motor speech generation that matches the heard speech. Our results suggest that interactions between perceptual and motor processing of speech relies on a distributed network of temporal and motor regions rather than any specific anatomical landmark as suggested by some previous studies.