bluuebunny/crossref_metadata_2025_split huggingface dataset:
A one-step, tunable method of selective reactive sputter deposition as a wrinkling approach for silver/polydimethylsiloxane for electrically conductive pliable surfaces
Authors: Loh Joel Y. Y. , Zeineddine Ali , Shayegannia Moein , McNeil Robyn , McRae Liam , Kherani Nazir P. 
Published: August 2022

AbstractThe wrinkle period and morphology of a metal thin film on an elastic substrate is typically controlled by modifying the substrate before carrying out additional metal deposition steps. Herein, we show that a simultaneously selective and reactive sputtering plasma that modifies the surface of a polydimethylsiloxane (PDMS) substrate while not reacting with the metal during the deposition process decreases the wrinkle wavelength and induces additional wrinkling components and features such as ripples or folds. The selective reaction of the nitrogen plasma with PDMS functionalizes the siloxane surface into silicon oxynitride. This hardens the immediate surface of PDMS, with a quadratic increase in the Young’s modulus as a function of the sputtering flow ratio. The increase in the critical strain mismatch and the corresponding presence of folds in the nitrogen-modified wrinkled silver film form a suitable plasmonic platform for surface-enhanced Raman spectroscopy (SERS), yielding an enhancement factor of 4.8 × 105for detecting lipids. This enhancement is linked to the emergence of electromagnetic hotspots from surface plasmon polariton coupling between the folds/wrinkles, which in turn enables the detection of low concentrations of organics using SERS. Furthermore, when strained, the nitrogen-modified wrinkles enhance electrical conductivity by a factor of 12 compared with unmodified films. Finally, the optical properties of the substrate can be tuned by altering the N2content. The simple addition of nonreactive nitrogen to silver sputtering enables simultaneous PDMS hardening and growth of the silver film and together provide a new avenue for tuning wrinkling parameters and enhancing the electrical conductivity of pliable surfaces.
Methylation of HBP1 by PRMT1 promotes tumor progression by regulating actin cytoskeleton remodeling
Authors: Wang Jiyin , Yang Ruixiang , Cheng Yuning , Zhou Yue , Zhang Tongjia , Wang Shujie , Li Hui , Jiang Wei , Zhang Xiaowei 
Published: August 2022

AbstractHBP1 is a sequence-specific transcription factor which generally considered as a crucial growth inhibitor. Posttranslational modification of HBP1 is vital for its function. In this study, we demonstrate that HBP1 is methylated at R378 by PRMT1, which decreases HBP1 protein stability by promoting its ubiquitination and proteasome-mediated degradation. PRMT1-mediated methylation of HBP1 alleviates the repressive effects of HBP1 on tumor metastasis and growth. GSN is identified as a novel target gene of HBP1. Methylation of HBP1 promotes actin cytoskeleton remodeling, glycolysis and tumor progression by downregulating GSN (a vital actin-binding protein) levels. The methylated HBP1-GSN axis is associated with the clinical outcomes of cancer patients. This investigation elucidates the mechanism of how methylated HBP1 facilitates actin cytoskeleton remodeling, thus attenuates its tumor-suppressive function and promotes tumor progression. Targeting methylated HBP1-GSN axis may provide a therapeutic strategy for cancer.
“Difficult” dental patients: a grounded theory study of dental staff’s experiences
Authors: Alvenfors Adam , Velic Mersiha , Marklund Bertil , Kylén Sven , Lingström Peter , Bernson Jenny 
Published: August 2022

Abstract
Introduction
The “difficult” patient is a well-known and potentially negative character in various care contexts.

Objectives
This study aimed to generate a conceptual framework explaining the main concerns about “difficult” dental patients, and obtain a deeper understanding of their characteristics, how they affect the dental staff and how the staff think and act in order to manage these patients.

Methods
Ten interviews were conducted with professional dental caregivers, including dentists, dental hygienists, and dental nurses. The audio-recorded interviews were transcribed and analyzed in accordance with the principles of grounded theory.

Results
The main concern regarding “difficult” dental patients generated a framework of seven descriptive interrelated lower-level categories grounded in the data, subsumed in the core category “balancing subjective difficulties”. The informants perceived the possession of “showing interaction difficulties” and “having bio-psycho-social complexity”, as characteristic features of “difficult” patients, who could further adversely affect the dental staff by “evoking negative emotions and behaviors”, “hampering self-esteem and job satisfaction”, and “impairing life and health in general”. To manage the dental care of these patients, the staff used strategies aimed at “activating internal and external resources” and “creating adaptive treatment relations” with patients.

Conclusions
The dental staff’s meaning of the phenomenon of “difficult” dental patients points to specific characteristics, effects, and handling strategies. The core category captures the contradictory dynamics of characteristics and affects as these concepts seem interrelated to the caregivers’ handling capacity. The dental staff’s possibility of handling the main concern through balancing subjective difficulties depends on contextual conditions regarding time, to bring the patient and/or oneself at the center of attention. This indicates a need for further research regarding dental interactions and studies generalizing the outlook on “difficult” dental patients.
OTUD1 deubiquitinase regulates NF-κB- and KEAP1-mediated inflammatory responses and reactive oxygen species-associated cell death pathways
Authors: Oikawa Daisuke , Gi Min , Kosako Hidetaka , Shimizu Kouhei , Takahashi Hirotaka , Shiota Masayuki , Hosomi Shuhei , Komakura Keidai , Wanibuchi Hideki , Tsuruta Daisuke , Sawasaki Tatsuya , Tokunaga Fuminori 
Published: August 2022

AbstractDeubiquitinating enzymes (DUBs) regulate numerous cellular functions by removing ubiquitin modifications. We examined the effects of 88 human DUBs on linear ubiquitin chain assembly complex (LUBAC)-induced NF-κB activation, and identified OTUD1 as a potent suppressor. OTUD1 regulates the canonical NF-κB pathway by hydrolyzing K63-linked ubiquitin chains from NF-κB signaling factors, including LUBAC. OTUD1 negatively regulates the canonical NF-κB activation, apoptosis, and necroptosis, whereas OTUD1 upregulates the interferon (IFN) antiviral pathway. Mass spectrometric analysis showed that OTUD1 binds KEAP1, and the N-terminal intrinsically disordered region of OTUD1, which contains an ETGE motif, is indispensable for the KEAP1-binding. Indeed, OTUD1 is involved in the KEAP1-mediated antioxidant response and reactive oxygen species (ROS)-induced cell death, oxeiptosis. In Otud1−/−-mice, inflammation, oxidative damage, and cell death were enhanced in inflammatory bowel disease, acute hepatitis, and sepsis models. Thus, OTUD1 is a crucial regulator for the inflammatory, innate immune, and oxidative stress responses and ROS-associated cell death pathways.
Development of high-energy non-aqueous lithium-sulfur batteries via redox-active interlayer strategy
Authors: Lee Byong-June , Zhao Chen , Yu Jeong-Hoon , Kang Tong-Hyun , Park Hyean-Yeol , Kang Joonhee , Jung Yongju , Liu Xiang , Li Tianyi , Xu Wenqian , Zuo Xiao-Bing , Xu Gui-Liang , Amine Khalil , Yu Jong-Sung 
Published: August 2022

AbstractLithium-sulfur batteries have theoretical specific energy higher than state-of-the-art lithium-ion batteries. However, from a practical perspective, these batteries exhibit poor cycle life and low energy content owing to the polysulfides shuttling during cycling. To tackle these issues, researchers proposed the use of redox-inactive protective layers between the sulfur-containing cathode and lithium metal anode. However, these interlayers provide additional weight to the cell, thus, decreasing the practical specific energy. Here, we report the development and testing of redox-active interlayers consisting of sulfur-impregnated polar ordered mesoporous silica. Differently from redox-inactive interlayers, these redox-active interlayers enable the electrochemical reactivation of the soluble polysulfides, protect the lithium metal electrode from detrimental reactions via silica-polysulfide polar-polar interactions and increase the cell capacity. Indeed, when tested in a non-aqueous Li-S coin cell configuration, the use of the interlayer enables an initial discharge capacity of about 8.5 mAh cm−2 (for a total sulfur mass loading of 10 mg cm−2) and a discharge capacity retention of about 64 % after 700 cycles at 335 mA g−1 and 25 °C.
Acetate reprograms gut microbiota during alcohol consumption
Authors: Martino Cameron , Zaramela Livia S. , Gao Bei , Embree Mallory , Tarasova Janna , Parker Seth J. , Wang Yanhan , Chu Huikuan , Chen Peng , Lee Kuei-Chuan , Galzerani Daniela Domingos , Gengatharan Jivani M. , Lekbua Asama , Neal Maxwell , Knight Rob , Tsukamoto Hidekazu , Metallo Christian M. , Schnabl Bernd , Zengler Karsten 
Published: August 2022

AbstractLiver damage due to chronic alcohol use is among the most prevalent liver diseases. Alcohol consumption frequency is a strong factor of microbiota variance. Here we use isotope labeled [1-13C] ethanol, metagenomics, and metatranscriptomics in ethanol-feeding and intragastric mouse models to investigate the metabolic impacts of alcohol consumption on the gut microbiota. First, we show that although stable isotope labeled [1-13C] ethanol contributes to fatty acid pools in the liver, plasma, and cecum contents of mice, there is no evidence of ethanol metabolism by gut microbiota ex vivo under anaerobic conditions. Next, we observe through metatranscriptomics that the gut microbiota responds to ethanol-feeding by activating acetate dissimilation, not by metabolizing ethanol directly. We demonstrate that blood acetate concentrations are elevated during ethanol consumption. Finally, by increasing systemic acetate levels with glyceryl triacetate supplementation, we do not observe any impact on liver disease, but do induce similar gut microbiota alterations as chronic ethanol-feeding in mice. Our results show that ethanol is not directly metabolized by the gut microbiota, and changes in the gut microbiota linked to ethanol are a side effect of elevated acetate levels. De-trending for these acetate effects may be critical for understanding gut microbiota changes that cause alcohol-related liver disease.
Programmable RNA targeting by bacterial Argonaute nucleases with unconventional guide binding and cleavage specificity
Authors: Lisitskaya Lidiya , Shin Yeonoh , Agapov Aleksei , Olina Anna , Kropocheva Ekaterina , Ryazansky Sergei , Aravin Alexei A. , Esyunina Daria , Murakami Katsuhiko S. , Kulbachinskiy Andrey 
Published: August 2022

AbstractArgonaute proteins are programmable nucleases that have defense and regulatory functions in both eukaryotes and prokaryotes. All known prokaryotic Argonautes (pAgos) characterized so far act on DNA targets. Here, we describe a new class of pAgos that uniquely use DNA guides to process RNA targets. The biochemical and structural analysis of Pseudooceanicola lipolyticus pAgo (PliAgo) reveals an unusual organization of the guide binding pocket that does not rely on divalent cations and the canonical set of contacts for 5’-end interactions. Unconventional interactions of PliAgo with the 5’-phosphate of guide DNA define its new position within pAgo and shift the site of target RNA cleavage in comparison with known Argonautes. The specificity for RNA over DNA is defined by ribonucleotide residues at the cleavage site. The analysed pAgos sense mismatches and modifications in the RNA target. The results broaden our understanding of prokaryotic defense systems and extend the spectrum of programmable nucleases with potential use in RNA technology.
G protein coupling and activation of the metabotropic GABAB heterodimer
Authors: Yang Moon Young , Kim Soo-Kyung , Goddard William A. 
Published: August 2022

AbstractMetabotropic γ-aminobutyric acid receptor (GABABR), a class C G protein-coupled receptor (GPCR) heterodimer, plays a crucial role in the central nervous system. Cryo-electron microscopy studies revealed a drastic conformational change upon activation and a unique G protein (GP) binding mode. However, little is known about the mechanism for GP coupling and activation for class C GPCRs. Here, we use molecular metadynamics computations to predict the mechanism by which the inactive GP induces conformational changes in the GABABR transmembrane domain (TMD) to form an intermediate pre-activated state. We find that the inactive GP first interacts with TM3, which further leads to the TMD rearrangement and deeper insertion of the α5 helix that causes the Gα subunit to open, releasing GDP, and forming the experimentally observed activated structure. This mechanism provides fresh insights into the mechanistic details of class C GPCRs activation expected to be useful for designing selective agonists and antagonists.
Photonic crystal enhanced fluorescence emission and blinking suppression for single quantum dot digital resolution biosensing
Authors: Xiong Yanyu , Huang Qinglan , Canady Taylor D. , Barya Priyash , Liu Shengyan , Arogundade Opeyemi H. , Race Caitlin M. , Che Congnyu , Wang Xiaojing , Zhou Lifeng , Wang Xing , Kohli Manish , Smith Andrew M. , Cunningham Brian T. 
Published: August 2022

AbstractWhile nanoscale quantum emitters are effective tags for measuring biomolecular interactions, their utilities for applications that demand single-unit observations are limited by the requirements for large numerical aperture (NA) objectives, fluorescence intermittency, and poor photon collection efficiency resulted from omnidirectional emission. Here, we report a nearly 3000-fold signal enhancement achieved through multiplicative effects of enhanced excitation, highly directional extraction, quantum efficiency improvement, and blinking suppression through a photonic crystal (PC) surface. The approach achieves single quantum dot (QD) sensitivity with high signal-to-noise ratio, even when using a low-NA lens and an inexpensive optical setup. The blinking suppression capability of the PC improves the QDs on-time from 15% to 85% ameliorating signal intermittency. We developed an assay for cancer-associated miRNA biomarkers with single-molecule resolution, single-base mutation selectivity, and 10-attomolar detection limit. Additionally, we observed differential surface motion trajectories of QDs when their surface attachment stringency is altered by changing a single base in a cancer-specific miRNA sequence.
A 33-residue peptide tag increases solubility and stability of Escherichia coli produced single-chain antibody fragments
Authors: Wang Yang , Yuan Wenjie , Guo Siqi , Li Qiqi , Chen Xiaomei , Li Cheng , Liu Qianying , Sun Lei , Chen Zhenguo , Yuan Zhenghong , Luo Cheng , Chen Shijie , Tong Shuping , Nassal Michael , Wen Yu-Mei , Wang Yong-Xiang 
Published: August 2022

AbstractSingle-chain variable fragments (scFvs), composed of variable domains of heavy and light chains of an antibody joined by a linker, share antigen binding capacity with their parental antibody. Due to intrinsically low solubility and stability, only two Escherichia coli-produced scFvs have been approved for therapy. Here we report that a 33-residue peptide, termed P17 tag, increases the solubility of multiple scFvs produced in Escherichia coli SHuffle strain by up to 11.6 fold. Hydrophilic sequence, especially charged residues, but not the predicted α-helical secondary structure of P17 tag, contribute to the solubility enhancement. Notably, the P17 tag elevates the thermostability of scFv as efficiently as intra-domain disulfide bonds. Moreover, a P17-tagged scFv targeting hepatitis B virus surface proteins shows over two-fold higher antigen-binding affinity and virus-neutralizing activity than the untagged version. These data strongly suggest a type I intramolecular chaperone-like activity of the P17 tag. Hence, the P17 tag could benefit the research, production, and application of scFv.
Adaptation to chronic ER stress enforces pancreatic β-cell plasticity
Authors: Chen Chien-Wen , Guan Bo-Jhih , Alzahrani Mohammed R. , Gao Zhaofeng , Gao Long , Bracey Syrena , Wu Jing , Mbow Cheikh A. , Jobava Raul , Haataja Leena , Zalavadia Ajay H. , Schaffer Ashleigh E. , Lee Hugo , LaFramboise Thomas , Bederman Ilya , Arvan Peter , Mathews Clayton E. , Gerling Ivan C. , Kaestner Klaus H. , Tirosh Boaz , Engin Feyza , Hatzoglou Maria 
Published: August 2022

AbstractPancreatic β-cells are prone to endoplasmic reticulum (ER) stress due to their role in insulin secretion. They require sustainable and efficient adaptive stress responses to cope with this stress. Whether episodes of chronic stress directly compromise β-cell identity is unknown. We show here under reversible, chronic stress conditions β-cells undergo transcriptional and translational reprogramming associated with impaired expression of regulators of β-cell function and identity. Upon recovery from stress, β-cells regain their identity and function, indicating a high degree of adaptive plasticity. Remarkably, while β-cells show resilience to episodic ER stress, when episodes exceed a threshold, β-cell identity is gradually lost. Single cell RNA-sequencing analysis of islets from type 1 diabetes patients indicates severe deregulation of the chronic stress-adaptation program and reveals novel biomarkers of diabetes progression. Our results suggest β-cell adaptive exhaustion contributes to diabetes pathogenesis.
Acute health-related quality of life outcomes and systemic inflammatory markers following contemporary breast cancer surgery
Authors: Radin Arielle S. , Bower Julienne E. , Irwin Michael R. , Asher Arash , Hurvitz Sara A. , Cole Steve W. , Crespi Catherine M. , Ganz Patricia A. 
Published: August 2022

AbstractContemporary breast cancer surgical procedures vary greatly by the amount of tissue removed, anesthesia time, and reconstruction. Despite historical literature comparing the health-related quality of life (HRQOL) after lumpectomy and mastectomy, HRQOL data are limited regarding contemporary surgical procedures. Further, biological processes (e.g., inflammation) associated with HRQOL outcomes have not been described. We conducted two studies to examine differences in post-operative physical and mental functioning, pain, fatigue, and systemic inflammatory markers including interleukin (IL)-6, tumor necrosis factor (TNF)-α, and C-reactive protein (CRP) in women with early-stage breast cancer. Study 1 assessed women before and after surgery (n = 27) and Study 2 used a large cross-sectional sample (n = 240) to confirm findings from Study 1 and included a no-surgery comparison group. In Study 1, women who received mastectomy had lower physical functioning than lumpectomy (ps < 0.05), and those who received bilateral mastectomy had worse pain (p < 0.01) and fatigue (p = 0.029) than lumpectomy. Results were replicated in Study 2: mastectomy groups exhibited poorer physical functioning (ps < 0.01) and greater pain (ps < 0.001) than lumpectomy, and bilateral mastectomy was associated with worse fatigue (p < 0.05). Women who received bilateral mastectomy had higher levels of CRP than lumpectomy (p < 0.01) and higher TNF-α than the no-surgery group (p < 0.05). All surgery groups exhibited higher IL-6 than no-surgery (ps < 0.05). More extensive surgery is associated with poorer postoperative HRQOL. As compared to lumpectomy and no-surgery, mastectomy is associated with higher concentrations of systemic inflammatory markers.
Mass spectrometry of short peptides reveals common features of metazoan peptidergic neurons
Authors: Hayakawa Eisuke , Guzman Christine , Horiguchi Osamu , Kawano Chihiro , Shiraishi Akira , Mohri Kurato , Lin Mei-Fang , Nakamura Ryotaro , Nakamura Ryo , Kawai Erina , Komoto Shinya , Jokura Kei , Shiba Kogiku , Shigenobu Shuji , Satake Honoo , Inaba Kazuo , Watanabe Hiroshi 
Published: August 2022

AbstractThe evolutionary origins of neurons remain unknown. Although recent genome data of extant early-branching animals have shown that neural genes existed in the common ancestor of animals, the physiological and genetic properties of neurons in the early evolutionary phase are still unclear. Here, we performed a mass spectrometry-based comprehensive survey of short peptides from early-branching lineages Cnidaria, Porifera and Ctenophora. We identified a number of mature ctenophore neuropeptides that are expressed in neurons associated with sensory, muscular and digestive systems. The ctenophore peptides are stored in vesicles in cell bodies and neurites, suggesting volume transmission similar to that of cnidarian and bilaterian peptidergic systems. A comparison of genetic characteristics revealed that the peptide-expressing cells of Cnidaria and Ctenophora express the vast majority of genes that have pivotal roles in maturation, secretion and degradation of neuropeptides in Bilateria. Functional analysis of neuropeptides and prediction of receptors with machine learning demonstrated peptide regulation of a wide range of target effector cells, including cells of muscular systems. The striking parallels between the peptidergic neuronal properties of Cnidaria and Bilateria and those of Ctenophora, the most basal neuron-bearing animals, suggest a common evolutionary origin of metazoan peptidergic nervous systems.
Connection between high pore-fluid pressure and frictional instability at tsunamigenic plate boundary fault of 2011 Tohoku-Oki earthquake
Authors: Jamali Hondori Ehsan , Park Jin-Oh 
Published: August 2022

AbstractThe 2011 Tohoku-Oki earthquake (M 9.0) rupture propagated along a shallow plate boundary thrust fault (i.e. decollement) to the trench, displaced the seafloor, and triggered a devastating tsunami. Physical properties of the underthrust sediments which control the rupture propagation are yet poorly known. We use a 2D seismic dataset to build velocity model for imaging and apply reverse time migration. We then calculate pore-fluid pressure along the decollement as the top boundary of underthrust sediments, and along the backstop interface as the boundary between undeformed structures in the continental plate and the severely deformed sediments in the accretionary prism. The results show that within horizontal distance of 40–22 km toward the trench, pore-fluid pressure is 82–60% higher than the hydrostatic pressure for both decollement and backstop interface. It then reduces to hydrostatic level for the backstop interface but remains 60–40% higher than hydrostatic level for the decollement, causing frictional instability in favor of fault rupture along the decollement. We report for the first time, by our knowledge, detailed seismic images of fluid-rich trapped bucket sediments, quantitative stress states, and fluid drainage conditions at shallow tsunamigenic portion of the Japan Trench, which are consistent with the seafloor and borehole observations.