bluuebunny/crossref_metadata_2025_split huggingface dataset:
sGRP78 enhances selective autophagy of monomeric TLR4 to regulate myeloid cell death
Authors: Wu Zhenghao , Xu Zhuoshuo , Zhou Xiaoqi , Li Heli , Zhao Liang , Lv Yibing , Guo Yanyan , Shen Guanxin , He Yong , Lei Ping 
Published: July 2022

AbstractSoluble glucose regulated protein 78 (sGRP78) has long been suggested as a mediator resolution of inflammation. We previously reported that sGRP78 induced the rapid endocytosis of TLR4 with defective TLR4 signaling. To elucidate the underlying mechanisms, in this study, we investigated how sGRP78 influenced the behavior and trafficking of TLR4 in myeloid cells. It was found that sGRP78 promoted LPS endocytosis with monomeric TLR4. This internalized monomeric TLR4 formed complexes with p62–LC3, and was degraded in autolysosomes. Furthermore, the sGRP78-enhanced autophagy-dependent TLR4 degradation caused apoptosis and ferroptosis in myeloid cells, contributing to the sGRP78-mediated resolution of inflammation. These reports establish innovative mechanisms for endotoxin clearance and immune regulation by TLR4 degradation, linking innate immunity with multiple ancient processes, including autophagy, apoptosis, and ferroptosis, together through a shared resolution-associated molecular pattern (RAMP)—sGRP78.
Fluorescence turn on amine detection in a cationic covalent organic framework
Authors: Das Gobinda , Garai Bikash , Prakasam Thirumurugan , Benyettou Farah , Varghese Sabu , Sharma Sudhir Kumar , Gándara Felipe , Pasricha Renu , Baias Maria , Jagannathan Ramesh , Saleh Na’il , Elhabiri Mourad , Olson Mark A. , Trabolsi Ali 
Published: July 2022

AbstractIonic covalent organic frameworks (iCOFs) are new examples of porous materials and have shown great potential for various applications. When functionalized with suitable emission sites, guest uptake via the ionic moieties of iCOFs can cause a significant change in luminescence, making them excellent candidates for chemosensors. In here, we present a luminescence sensor in the form of an ionic covalent organic framework (TGH+•PD) composed of guanidinium and phenanthroline moieties for the detection of ammonia and primary aliphatic amines. TGH+•PD exhibits strong emission enhancement in the presence of selective primary amines due to the suppression of intramolecular charge transfer (ICT) with an ultra-low detection limit of 1.2 × 10‒7M for ammonia. The presence of ionic moieties makes TGH+•PD highly dispersible in water, while deprotonation of the guanidinium moiety by amines restricts its ICT process and signals their presence by enhanced fluorescence emission. The presence of ordered pore walls introduces size selectivity among analyte molecules, and the iCOF has been successfully used to monitor meat products that release biogenic amine vapors upon decomposition due to improper storage.
Mutations in DNA polymerase δ subunit 1 co-segregate with CMD2-type resistance to Cassava Mosaic Geminiviruses
Authors: Lim Yi-Wen , Mansfeld Ben N. , Schläpfer Pascal , Gilbert Kerrigan B. , Narayanan Narayanan N. , Qi Weihong , Wang Qi , Zhong Zhenhui , Boyher Adam , Gehan Jackson , Beyene Getu , Lin Zuh-Jyh Daniel , Esuma Williams , Feng Suhua , Chanez Christelle , Eggenberger Nadine , Adiga Gerald , Alicai Titus , Jacobsen Steven E. , Taylor Nigel J. , Gruissem Wilhelm , Bart Rebecca S. 
Published: July 2022

AbstractCassava mosaic disease (CMD) suppresses cassava yields across the tropics. The dominantCMD2locus confers resistance to cassava mosaic geminiviruses. It has been reported that CMD2-type landraces lose resistance after regeneration through de novo morphogenesis. As full genome bisulfite sequencing failed to uncover an epigenetic mechanism for this loss of resistance, whole genome sequencing and genetic variant analysis was performed and the CMD2 locus was fine-mapped to a 190 kilobase interval. Collectively, these data indicate that CMD2-type resistance is caused by a nonsynonymous, single nucleotide polymorphism inDNA polymerase δ subunit 1(MePOLD1) located within this region. Virus-induced gene silencing ofMePOLD1in a CMD-susceptible cassava variety produced a recovery phenotype typical of CMD2-type resistance. Analysis of other CMD2-type cassava varieties identified additional candidate resistance alleles withinMePOLD1. Genetic variation ofMePOLD1, therefore, could represent an important genetic resource for resistance breeding and/or genome editing, and elucidating mechanisms of resistance to geminiviruses.
Characterization of core fucosylation via sequential enzymatic treatments of intact glycopeptides and mass spectrometry analysis
Authors: Cao Liwei , Lih T. Mamie , Hu Yingwei , Schnaubelt Michael , Chen Shao-Yung , Zhou Yangying , Guo Chuanyu , Dong Mingming , Yang Weiming , Eguez Rodrigo Vargas , Chen Lijun , Clark David J. , Sodhi Akrit , Li Qing Kay , Zhang Hui 
Published: July 2022

AbstractCore fucosylation of N-linked glycoproteins has been linked to the functions of glycoproteins in physiological and pathological processes. However, quantitative characterization of core fucosylation remains challenging due to the complexity and heterogeneity of N-linked glycosylation. Here we report a mass spectrometry-based method that employs sequential treatment of intact glycopeptides with enzymes (STAGE) to analyze site-specific core fucosylation of glycoproteins. The STAGE method utilizes Endo F3 followed by PNGase F treatment to generate mass signatures for glycosites that are formerly modified by core fucosylated N-linked glycans. We benchmark the STAGE method and use it to characterize site specific core fucosylation of glycoproteins from human hepatocellular carcinoma and pancreatic ductal adenocarcinoma, resulting in the identification of 1130 and 782 core fucosylated glycosites, respectively. These results indicate that our STAGE method enables quantitative characterization of core fucosylation events from complex protein mixtures, which may benefit our understanding of core fucosylation functions in various diseases.
TGFβ reprograms TNF stimulation of macrophages towards a non-canonical pathway driving inflammatory osteoclastogenesis
Authors: Xia Yuhan , Inoue Kazuki , Du Yong , Baker Stacey J. , Reddy E. Premkumar , Greenblatt Matthew B. , Zhao Baohong 
Published: July 2022

AbstractIt is well-established that receptor activator of NF-κB ligand (RANKL) is the inducer of physiological osteoclast differentiation. However, the specific drivers and mechanisms driving inflammatory osteoclast differentiation under pathological conditions remain obscure. This is especially true given that inflammatory cytokines such as tumor necrosis factor (TNF) demonstrate little to no ability to directly drive osteoclast differentiation. Here, we found that transforming growth factor β (TGFβ) priming enables TNF to effectively induce osteoclastogenesis, independently of the canonical RANKL pathway. Lack of TGFβ signaling in macrophages suppresses inflammatory, but not basal, osteoclastogenesis and bone resorption in vivo. Mechanistically, TGFβ priming reprograms the macrophage response to TNF by remodeling chromatin accessibility and histone modifications, and enables TNF to induce a previously unrecognized non-canonical osteoclastogenic program, which includes suppression of the TNF-induced IRF1-IFNβ-IFN-stimulated-gene axis, IRF8 degradation and B-Myb induction. These mechanisms are active in rheumatoid arthritis, in which TGFβ level is elevated and correlates with osteoclast activity. Our findings identify a TGFβ/TNF-driven inflammatory osteoclastogenic program, and may lead to development of selective treatments for inflammatory osteolysis.
Mode-pairing quantum key distribution
Authors: Zeng Pei , Zhou Hongyi , Wu Weijie , Ma Xiongfeng 
Published: July 2022

AbstractQuantum key distribution — the establishment of information-theoretically secure keys based on quantum physics — is mainly limited by its practical performance, which is characterised by the dependence of the key rate on the channel transmittance R(η). Recently, schemes based on single-photon interference have been proposed to improve the key rate to $$R=O(\sqrt{\eta })$$
R
=
O

(

η

)

by overcoming the point-to-point secret key capacity bound with interferometers. Unfortunately, all of these schemes require challenging global phase locking to realise a stable long-arm single-photon interferometer with a precision of approximately 100 nm over fibres that are hundreds of kilometres long. Aiming to address this problem, we propose a mode-pairing measurement-device-independent quantum key distribution scheme in which the encoded key bits and bases are determined during data post-processing. Using conventional second-order interference, this scheme can achieve a key rate of $$R=O(\sqrt{\eta })$$
R
=
O

(

η

)

without global phase locking when the local phase fluctuation is mild. We expect this high-performance scheme to be ready-to-implement with off-the-shelf optical devices.
Audiovisual adaptation is expressed in spatial and decisional codes
Authors: Aller Máté , Mihalik Agoston , Noppeney Uta 
Published: July 2022

AbstractThe brain adapts dynamically to the changing sensory statistics of its environment. Recent research has started to delineate the neural circuitries and representations that support this cross-sensory plasticity. Combining psychophysics and model-based representational fMRI and EEG we characterized how the adult human brain adapts to misaligned audiovisual signals. We show that audiovisual adaptation is associated with changes in regional BOLD-responses and fine-scale activity patterns in a widespread network from Heschl’s gyrus to dorsolateral prefrontal cortices. Audiovisual recalibration relies on distinct spatial and decisional codes that are expressed with opposite gradients and time courses across the auditory processing hierarchy. Early activity patterns in auditory cortices encode sounds in a continuous space that flexibly adapts to misaligned visual inputs. Later activity patterns in frontoparietal cortices code decisional uncertainty consistent with these spatial transformations. Our findings suggest that regions within the auditory processing hierarchy multiplex spatial and decisional codes to adapt flexibly to the changing sensory statistics in the environment.
Light sources with bias tunable spectrum based on van der Waals interface transistors
Authors: Henck Hugo , Mauro Diego , Domaretskiy Daniil , Philippi Marc , Memaran Shahriar , Zheng Wenkai , Lu Zhengguang , Shcherbakov Dmitry , Lau Chun Ning , Smirnov Dmitry , Balicas Luis , Watanabe Kenji , Taniguchi Takashi , Fal’ko Vladimir I. , Gutiérrez-Lezama Ignacio , Ubrig Nicolas , Morpurgo Alberto F. 
Published: July 2022

AbstractLight-emitting electronic devices are ubiquitous in key areas of current technology, such as data communications, solid-state lighting, displays, and optical interconnects. Controlling the spectrum of the emitted light electrically, by simply acting on the device bias conditions, is an important goal with potential technological repercussions. However, identifying a material platform enabling broad electrical tuning of the spectrum of electroluminescent devices remains challenging. Here, we propose light-emitting field-effect transistors based on van der Waals interfaces of atomically thin semiconductors as a promising class of devices to achieve this goal. We demonstrate that large spectral changes in room-temperature electroluminescence can be controlled both at the device assembly stage –by suitably selecting the material forming the interfaces– and on-chip, by changing the bias to modify the device operation point. Even though the precise relation between device bias and kinetics of the radiative transitions remains to be understood, our experiments show that the physical mechanism responsible for light emission is robust, making these devices compatible with simple large areas device production methods.
TET1 dioxygenase is required for FOXA2-associated chromatin remodeling in pancreatic beta-cell differentiation
Authors: Li Jianfang , Wu Xinwei , Ke Jie , Lee Minjung , Lan Qingping , Li Jia , Yu Jianxiu , Huang Yun , Sun De-Qiang , Xie Ruiyu 
Published: July 2022

AbstractExisting knowledge of the role of epigenetic modifiers in pancreas development has exponentially increased. However, the function of TET dioxygenases in pancreatic endocrine specification remains obscure. We set out to tackle this issue using a human embryonic stem cell (hESC) differentiation system, in which TET1/TET2/TET3 triple knockout cells display severe defects in pancreatic β-cell specification. The integrative whole-genome analysis identifies unique cell-type-specific hypermethylated regions (hyper-DMRs) displaying reduced chromatin activity and remarkable enrichment of FOXA2, a pioneer transcription factor essential for pancreatic endoderm specification. Intriguingly, TET depletion leads to significant changes in FOXA2 binding at the pancreatic progenitor stage, in which gene loci with decreased FOXA2 binding feature low levels of active chromatin modifications and enriches for bHLH motifs. Transduction of full-length TET1 but not the TET1-catalytic-domain in TET-deficient cells effectively rescues β-cell differentiation accompanied by restoring PAX4 hypomethylation. Taking these findings together with the defective generation of functional β-cells upon TET1-inactivation, our study unveils an essential role of TET1-dependent demethylation in establishing β-cell identity. Moreover, we discover a physical interaction between TET1 and FOXA2 in endodermal lineage intermediates, which provides a mechanistic clue regarding the complex crosstalk between TET dioxygenases and pioneer transcription factors in epigenetic regulation during pancreas specification.
Transcriptional programming in a Bacteroides consortium
Authors: Huang Brian D. , Groseclose Thomas M. , Wilson Corey J. 
Published: July 2022

AbstractBacteroides species are prominent members of the human gut microbiota. The prevalence and stability of Bacteroides in humans make them ideal candidates to engineer as programmable living therapeutics. Here we report a biotic decision-making technology in a community of Bacteroides (consortium transcriptional programming) with genetic circuit compression. Circuit compression requires systematic pairing of engineered transcription factors with cognate regulatable promoters. In turn, we demonstrate the compression workflow by designing, building, and testing all fundamental two-input logic gates dependent on the inputs isopropyl-β-D-1-thiogalactopyranoside and D-ribose. We then deploy complete sets of logical operations in five human donor Bacteroides, with which we demonstrate sequential gain-of-function control in co-culture. Finally, we couple transcriptional programs with CRISPR interference to achieve loss-of-function regulation of endogenous genes—demonstrating complex control over community composition in co-culture. This work provides a powerful toolkit to program gene expression in Bacteroides for the development of bespoke therapeutic bacteria.
Sex-specific regulation of inhibition and network activity by local aromatase in the mouse hippocampus
Authors: Hernández-Vivanco Alicia , Cano-Adamuz Nuria , Sánchez-Aguilera Alberto , González-Alonso Alba , Rodríguez-Fernández Alberto , Azcoitia Íñigo , de la Prida Liset Menendez , Méndez Pablo 
Published: July 2022

AbstractCognitive function relies on a balanced interplay between excitatory and inhibitory neurons (INs), but the impact of estradiol on IN function is not fully understood. Here, we characterize the regulation of hippocampal INs by aromatase, the enzyme responsible for estradiol synthesis, using a combination of molecular, genetic, functional and behavioral tools. The results show that CA1 parvalbumin-expressing INs (PV-INs) contribute to brain estradiol synthesis. Brain aromatase regulates synaptic inhibition through a mechanism that involves modification of perineuronal nets enwrapping PV-INs. In the female brain, aromatase modulates PV-INs activity, the dynamics of network oscillations and hippocampal-dependent memory. Aromatase regulation of PV-INs and inhibitory synapses is determined by the gonads and independent of sex chromosomes. These results suggest PV-INs are mediators of estrogenic regulation of behaviorally-relevant activity.
Highly robust and soft biohybrid mechanoluminescence for optical signaling and illumination
Authors: Li Chenghai , He Qiguang , Wang Yang , Wang Zhijian , Wang Zijun , Annapooranan Raja , Latz Michael I. , Cai Shengqiang 
Published: July 2022

AbstractBiohybrid is a newly emerging and promising approach to construct soft robotics and soft machines with novel functions, high energy efficiency, great adaptivity and intelligence. Despite many unique advantages of biohybrid systems, it is well known that most biohybrid systems have a relatively short lifetime, require complex fabrication process, and only remain functional with careful maintenance. Herein, we introduce a simple method to create a highly robust and power-free soft biohybrid mechanoluminescence, by encapsulating dinoflagellates, bioluminescent unicellular marine algae, into soft elastomeric chambers. The dinoflagellates retain their intrinsic bioluminescence, which is a near-instantaneous light response to mechanical forces. We demonstrate the robustness of various geometries of biohybrid mechanoluminescent devices, as well as potential applications such as visualizing external mechanical perturbations, deformation-induced illumination, and optical signaling in a dark environment. Our biohybrid mechanoluminescent devices are ultra-sensitive with fast response time and can maintain their light emission capability for weeks without special maintenance.
Assessing the effectiveness of orchestrated climate action from five years of summits
Authors: Chan Sander , Hale Thomas , Deneault Andrew , Shrivastava Manish , Mbeva Kennedy , Chengo Victoria , Atela Joanes 
Published: July 2022

AbstractAction-oriented summits like the 2018 Global Climate Action Summit and 2019 UN Climate Action Summit, have become a major feature of global climate governance. Their emphasis on cooperative initiatives by a host of non-state and local actors creates high expectations, especially when, according to the IPCC, governments’ policies still set the world on course for a disastrous 2.7 °C warming. While earlier studies have cautioned against undue optimism, empirical evidence on summits and their ability to leverage transnational capacities has been scarce. Here using a dataset of 276 climate initiatives we show important differences in output performance, with no improvement among initiatives associated with more recent summits. A summit’s focus on certain themes and an emphasis on minimal requirements for institutional robustness, however, can positively influence the effectiveness of transnational engagement. These results make an empirical contribution towards understanding the increasingly transnational nature of climate governance.
A randomised controlled trial of interventions for taxane-induced nail toxicity in women with early breast cancer
Authors: Morrison Audrey , Marshall-McKenna Rebecca , McFadyen Angus K. , Hutchison Cathy , Rice Ann-Marie , Stirling Lynne , McIlroy Pauline , Macpherson Iain R. 
Published: July 2022

AbstractOnycholysis and paronychia has been associated with chemotherapy treatment for women with breast cancer. Our primary aim was to investigate the effectiveness of different topical interventions to ameliorate nail toxicity. Secondary aims were to explore the full range and severity of possible nail changes associated with taxane-based chemotherapy and the specific impact this had on quality of life, using two novel measures. This was an exploratory randomised controlled trial of three topical interventions (standard care, nail polish or specialist nail drops) for the prevention or reduction of nail changes induced by taxane-based chemotherapy. Outcomes included nail toxicity assessed at three time points (baseline, 3 weeks and 3 months post completion of chemotherapy) using two novel clinical tools (NToX-G12, NToX-QoL) and the Common Terminology Criteria for Adverse Events (CTCAE v3) and EQ-5D-5L. A total of 105 women were recruited (35 in each arm) and monitored up to three months post completion of chemotherapy. Almost 20% of patients were over the age of 60 years. There were 26 withdrawals, the majority from the nail polish arm. Residual Maximum Likelihood REML analysis indicated a significant arm, time and interaction effect for each intervention (p < 0.001). Less nail toxicity was observed in patients receiving specialist nail drops or standard care arms in comparison to those using nail polish. This study provides evidence to support clinicians’ suggestions on nail care recommendations based on the patients’ needs and preferences. Future investigations into comparing or combining cryotherapy and topical solutions that can support patient’s decisions are warranted.
Return of large fin whale feeding aggregations to historical whaling grounds in the Southern Ocean
Authors: Herr Helena , Viquerat Sacha , Devas Fredi , Lees Abigail , Wells Lucy , Gregory Bertie , Giffords Ted , Beecham Dan , Meyer Bettina 
Published: July 2022

AbstractFin whales (Balaenoptera physalus quoyi) of the Southern Hemisphere were brought to near extinction by twentieth century industrial whaling. For decades, they had all but disappeared from previously highly frequented feeding grounds in Antarctic waters. Our dedicated surveys now confirm their return to ancestral feeding grounds, gathering at the Antarctic Peninsula in large aggregations to feed. We report on the results of an abundance survey and present the first scientific documentation of large fin whale feeding aggregations at Elephant Island, Antarctica, including the first ever video documentation. We interpret high densities, re-establishment of historical behaviours and the return to ancestral feeding grounds as signs for a recovering population. Recovery of a large whale population has the potential to augment primary productivity at their feeding grounds through the effects of nutrient recycling, known as 'the whale pump'. The recovery of fin whales in that area could thus restore ecosystem functions crucial for atmospheric carbon regulation in the world's most important ocean region for the uptake of anthropogenic CO2.
Structural and biochemical analyses of the flagellar expression regulator DegU from Listeria monocytogenes
Authors: Oh Han Byeol , Lee Su-jin , Yoon Sung-il 
Published: July 2022

AbstractListeria monocytogenes is a pathogenic bacterium that produces flagella, the locomotory organelles, in a temperature-dependent manner. At 37 °C inside humans, L. monocytogenes employs MogR to repress the expression of flagellar proteins, thereby preventing the production of flagella. However, in the low-temperature environment outside of the host, the antirepressor GmaR inactivates MogR, allowing flagellar formation. Additionally, DegU is necessary for flagellar expression at low temperatures. DegU transcriptionally activates the expression of GmaR and flagellar proteins by binding the operator DNA in the fliN-gmaR promoter as a response regulator of a two-component regulatory system. To determine the DegU-mediated regulation mechanism, we performed structural and biochemical analyses on the recognition of operator DNA by DegU. The DegU-DNA interaction is primarily mediated by a C-terminal DNA-binding domain (DBD) and can be fortified by an N-terminal receiver domain (RD). The DegU DBD adopts a tetrahelical helix-turn-helix structure and assembles into a dimer. The DegU DBD dimer recognizes the operator DNA using a positive patch. Unexpectedly, unlike typical response regulators, DegU interacts with operator DNA in both unphosphorylated and phosphorylated states with similar binding affinities. Therefore, we conclude that DegU is a noncanonical response regulator that is constitutively active irrespective of phosphorylation.