bluuebunny/crossref_metadata_2025_split huggingface dataset:
Porous carbon nanowire array for surface-enhanced Raman spectroscopy
Authors: Chen Nan , Xiao Ting-Hui , Luo Zhenyi , Kitahama Yasutaka , Hiramatsu Kotaro , Kishimoto Naoki , Itoh Tamitake , Cheng Zhenzhou , Goda Keisuke 
Published: September 2020

AbstractSurface-enhanced Raman spectroscopy (SERS) is a powerful tool for vibrational spectroscopy as it provides several orders of magnitude higher sensitivity than inherently weak spontaneous Raman scattering by exciting localized surface plasmon resonance (LSPR) on metal substrates. However, SERS can be unreliable for biomedical use since it sacrifices reproducibility, uniformity, biocompatibility, and durability due to its strong dependence on “hot spots”, large photothermal heat generation, and easy oxidization. Here, we demonstrate the design, fabrication, and use of a metal-free (i.e., LSPR-free), topologically tailored nanostructure composed of porous carbon nanowires in an array as a SERS substrate to overcome all these problems. Specifically, it offers not only high signal enhancement (~106) due to its strong broadband charge-transfer resonance, but also extraordinarily high reproducibility due to the absence of hot spots, high durability due to no oxidization, and high compatibility to biomolecules due to its fluorescence quenching capability.
Fault valving and pore pressure evolution in simulations of earthquake sequences and aseismic slip
Authors: Zhu Weiqiang , Allison Kali L. , Dunham Eric M. , Yang Yuyun 
Published: September 2020

AbstractFault-zone fluids control effective normal stress and fault strength. While most earthquake models assume a fixed pore fluid pressure distribution, geologists have documented fault valving behavior, that is, cyclic changes in pressure and unsteady fluid migration along faults. Here we quantify fault valving through 2-D antiplane shear simulations of earthquake sequences on a strike-slip fault with rate-and-state friction, upward Darcy flow along a permeable fault zone, and permeability evolution. Fluid overpressure develops during the interseismic period, when healing/sealing reduces fault permeability, and is released after earthquakes enhance permeability. Coupling between fluid flow, permeability and pressure evolution, and slip produces fluid-driven aseismic slip near the base of the seismogenic zone and earthquake swarms within the seismogenic zone, as ascending fluids pressurize and weaken the fault. This model might explain observations of late interseismic fault unlocking, slow slip and creep transients, swarm seismicity, and rapid pressure/stress transmission in induced seismicity sequences.
Combinatorial entropy behaviour leads to range selective binding in ligand-receptor interactions
Authors: Liu Meng , Apriceno Azzurra , Sipin Miguel , Scarpa Edoardo , Rodriguez-Arco Laura , Poma Alessandro , Marchello Gabriele , Battaglia Giuseppe , Angioletti-Uberti Stefano 
Published: September 2020

AbstractFrom viruses to nanoparticles, constructs functionalized with multiple ligands display peculiar binding properties that only arise from multivalent effects. Using statistical mechanical modelling, we describe here how multivalency can be exploited to achieve what we dub range selectivity, that is, binding only to targets bearing a number of receptors within a specified range. We use our model to characterise the region in parameter space where one can expect range selective targeting to occur, and provide experimental support for this phenomenon. Overall, range selectivity represents a potential path to increase the targeting selectivity of multivalent constructs.
MFSD7C switches mitochondrial ATP synthesis to thermogenesis in response to heme
Authors: Li Yingzhong , Ivica Nikola A. , Dong Ting , Papageorgiou Dimitrios P. , He Yanpu , Brown Douglas R. , Kleyman Marianna , Hu Guangan , Chen Walter W. , Sullivan Lucas B. , Del Rosario Amanda , Hammond Paula T. , Vander Heiden Matthew G. , Chen Jianzhu 
Published: September 2020

AbstractATP synthesis and thermogenesis are two critical outputs of mitochondrial respiration. How these outputs are regulated to balance the cellular requirement for energy and heat is largely unknown. Here we show that major facilitator superfamily domain containing 7C (MFSD7C) uncouples mitochondrial respiration to switch ATP synthesis to thermogenesis in response to heme. When heme levels are low, MSFD7C promotes ATP synthesis by interacting with components of the electron transport chain (ETC) complexes III, IV, and V, and destabilizing sarcoendoplasmic reticulum Ca2+-ATPase 2b (SERCA2b). Upon heme binding to the N-terminal domain, MFSD7C dissociates from ETC components and SERCA2b, resulting in SERCA2b stabilization and thermogenesis. The heme-regulated switch between ATP synthesis and thermogenesis enables cells to match outputs of mitochondrial respiration to their metabolic state and nutrient supply, and represents a cell intrinsic mechanism to regulate mitochondrial energy metabolism.
Copper catalysis at operando conditions—bridging the gap between single nanoparticle probing and catalyst-bed-averaging
Authors: Albinsson David , Boje Astrid , Nilsson Sara , Tiburski Christopher , Hellman Anders , Ström Henrik , Langhammer Christoph 
Published: September 2020

AbstractIn catalysis, nanoparticles enable chemical transformations and their structural and chemical fingerprints control activity. To develop understanding of such fingerprints, methods studying catalysts at realistic conditions have proven instrumental. Normally, these methods either probe the catalyst bed with low spatial resolution, thereby averaging out single particle characteristics, or probe an extremely small fraction only, thereby effectively ignoring most of the catalyst. Here, we bridge the gap between these two extremes by introducing highly multiplexed single particle plasmonic nanoimaging of model catalyst beds comprising 1000 nanoparticles, which are integrated in a nanoreactor platform that enables online mass spectroscopy activity measurements. Using the example of CO oxidation over Cu, we reveal how highly local spatial variations in catalyst state dynamics are responsible for contradicting information about catalyst active phase found in the literature, and identify that both surface and bulk oxidation state of a Cu nanoparticle catalyst dynamically mediate its activity.
Functional genetic encoding of sulfotyrosine in mammalian cells
Authors: He Xinyuan , Chen Yan , Beltran Daisy Guiza , Kelly Maia , Ma Bin , Lawrie Justin , Wang Feng , Dodds Eric , Zhang Limei , Guo Jiantao , Niu Wei 
Published: September 2020

AbstractProtein tyrosine O-sulfation (PTS) plays a crucial role in extracellular biomolecular interactions that dictate various cellular processes. It also involves in the development of many human diseases. Regardless of recent progress, our current understanding of PTS is still in its infancy. To promote and facilitate relevant studies, a generally applicable method is needed to enable efficient expression of sulfoproteins with defined sulfation sites in live mammalian cells. Here we report the engineering, in vitro biochemical characterization, structural study, and in vivo functional verification of a tyrosyl-tRNA synthetase mutant for the genetic encoding of sulfotyrosine in mammalian cells. We further apply this chemical biology tool to cell-based studies on the role of a sulfation site in the activation of chemokine receptor CXCR4 by its ligand. Our work will not only facilitate cellular studies of PTS, but also paves the way for economical production of sulfated proteins as therapeutic agents in mammalian systems.
Phase I clinical trial repurposing all-trans retinoic acid as a stromal targeting agent for pancreatic cancer
Authors: Kocher Hemant M. , Basu Bristi , Froeling Fieke E. M. , Sarker Debashis , Slater Sarah , Carlin Dominic , deSouza Nandita M. , De Paepe Katja N. , Goulart Michelle R. , Hughes Christine , Imrali Ahmet , Roberts Rhiannon , Pawula Maria , Houghton Richard , Lawrence Cheryl , Yogeswaran Yathushan , Mousa Kelly , Coetzee Carike , Sasieni Peter , Prendergast Aaron , Propper David J. 
Published: September 2020

AbstractPre-clinical models have shown that targeting pancreatic stellate cells with all-trans-retinoic-acid (ATRA) reprograms pancreatic stroma to suppress pancreatic ductal adenocarcinoma (PDAC) growth. Here, in a phase Ib, dose escalation and expansion, trial for patients with advanced, unresectable PDAC (n = 27), ATRA is re-purposed as a stromal-targeting agent in combination with gemcitabine-nab-paclitaxel chemotherapy using a two-step adaptive continual re-assessment method trial design. The maximum tolerated dose (MTD) and recommended phase 2 dose (RP2D, primary outcome) is the FDA/EMEA approved dose of gemcitabine-nab-paclitaxel along-with ATRA (45 mg/m2 orally, days 1–15/cycle). Dose limiting toxicity (DLT) is grade 4 thrombocytopenia (n = 2). Secondary outcomes show no detriment to ATRA pharmacokinetics.. Median overall survival for RP2D treated evaluable population, is 11.7 months (95%CI 8.6–15.7 m, n = 15, locally advanced (2) and metastatic (13)). Exploratory pharmacodynamics studies including changes in diffusion-weighted (DW)-MRI measured apparent diffusion coefficient after one cycle, and, modulation of cycle-specific serum pentraxin 3 levels over various cycles indicate stromal modulation. Baseline stromal-specific retinoid transport protein (FABP5, CRABP2) expression may be predicitve of response. Re-purposing ATRA as a stromal-targeting agent with gemcitabine-nab-paclitaxel is safe and tolerable. This combination will be evaluated in a phase II randomized controlled trial for locally advanced PDAC. Clinical trial numbers: EudraCT: 2015-002662-23; NCT03307148. Trial acronym: STARPAC.
Fabrication of a novel magnetic topological heterostructure and temperature evolution of its massive Dirac cone
Authors: Hirahara T. , Otrokov M. M. , Sasaki T. T. , Sumida K. , Tomohiro Y. , Kusaka S. , Okuyama Y. , Ichinokura S. , Kobayashi M. , Takeda Y. , Amemiya K. , Shirasawa T. , Ideta S. , Miyamoto K. , Tanaka K. , Kuroda S. , Okuda T. , Hono K. , Eremeev S. V. , Chulkov E. V. 
Published: September 2020

AbstractMaterials that possess nontrivial topology and magnetism is known to exhibit exotic quantum phenomena such as the quantum anomalous Hall effect. Here, we fabricate a novel magnetic topological heterostructure Mn4Bi2Te7/Bi2Te3 where multiple magnetic layers are inserted into the topmost quintuple layer of the original topological insulator Bi2Te3. A massive Dirac cone (DC) with a gap of 40–75 meV at 16 K is observed. By tracing the temperature evolution, this gap is shown to gradually decrease with increasing temperature and a blunt transition from a massive to a massless DC occurs around 200–250 K. Structural analysis shows that the samples also contain MnBi2Te4/Bi2Te3. Magnetic measurements show that there are two distinct Mn components in the system that corresponds to the two heterostructures; MnBi2Te4/Bi2Te3 is paramagnetic at 6 K while Mn4Bi2Te7/Bi2Te3 is ferromagnetic with a negative hysteresis (critical temperature ~20 K). This novel heterostructure is potentially important for future device applications.
Abiraterone acetate preferentially enriches for the gut commensal Akkermansia muciniphila in castrate-resistant prostate cancer patients
Authors: Daisley Brendan A. , Chanyi Ryan M. , Abdur-Rashid Kamilah , Al Kait F. , Gibbons Shaeley , Chmiel John A. , Wilcox Hannah , Reid Gregor , Anderson Amanda , Dewar Malcolm , Nair Shiva M. , Chin Joseph , Burton Jeremy P. 
Published: September 2020

AbstractAbiraterone acetate (AA) is an inhibitor of androgen biosynthesis, though this cannot fully explain its efficacy against androgen-independent prostate cancer. Here, we demonstrate that androgen deprivation therapy depletes androgen-utilizing Corynebacterium spp. in prostate cancer patients and that oral AA further enriches for the health-associated commensal, Akkermansia muciniphila. Functional inferencing elucidates a coinciding increase in bacterial biosynthesis of vitamin K2 (an inhibitor of androgen dependent and independent tumor growth). These results are highly reproducible in a host-free gut model, excluding the possibility of immune involvement. Further investigation reveals that AA is metabolized by bacteria in vitro and that breakdown components selectively impact growth. We conclude that A. muciniphila is a key regulator of AA-mediated restructuring of microbial communities, and that this species may affect treatment response in castrate-resistant cohorts. Ongoing initiatives aimed at modulating the colonic microbiota of cancer patients may consider targeted delivery of poorly absorbed selective bacterial growth agents.
Machine learning identifies scale-free properties in disordered materials
Authors: Yu Sunkyu , Piao Xianji , Park Namkyoo 
Published: September 2020

AbstractThe vast amount of design freedom in disordered systems expands the parameter space for signal processing. However, this large degree of freedom has hindered the deterministic design of disordered systems for target functionalities. Here, we employ a machine learning approach for predicting and designing wave-matter interactions in disordered structures, thereby identifying scale-free properties for waves. To abstract and map the features of wave behaviors and disordered structures, we develop disorder-to-localization and localization-to-disorder convolutional neural networks, each of which enables the instantaneous prediction of wave localization in disordered structures and the instantaneous generation of disordered structures from given localizations. We demonstrate that the structural properties of the network architectures lead to the identification of scale-free disordered structures having heavy-tailed distributions, thus achieving multiple orders of magnitude improvement in robustness to accidental defects. Our results verify the critical role of neural network structures in determining machine-learning-generated real-space structures and their defect immunity.
Laser-induced graphitization of polydopamine leads to enhanced mechanical performance while preserving multifunctionality
Authors: Lee Kyueui , Park Minok , Malollari Katerina G. , Shin Jisoo , Winkler Sally M. , Zheng Yuting , Park Jung Hwan , Grigoropoulos Costas P. , Messersmith Phillip B. 
Published: September 2020

AbstractPolydopamine (PDA) is a simple and versatile conformal coating material that has been proposed for a variety of uses; however in practice its performance is often hindered by poor mechanical properties and high roughness. Here, we show that blue-diode laser annealing dramatically improves mechanical performance and reduces roughness of PDA coatings. Laser-annealed PDA (LAPDA) was shown to be >100-fold more scratch resistant than pristine PDA and even better than hard inorganic substrates, which we attribute to partial graphitization and covalent coupling between PDA subunits during annealing. Moreover, laser annealing provides these benefits while preserving other attractive properties of PDA, as demonstrated by the superior biofouling resistance of antifouling polymer-grafted LAPDA compared to PDA modified with the same polymer. Our work suggests that laser annealing may allow the use of PDA in mechanically demanding applications previously considered inaccessible, without sacrificing the functional versatility that is so characteristic of PDA.
The social and environmental complexities of extracting energy transition metals
Authors: Lèbre Éléonore , Stringer Martin , Svobodova Kamila , Owen John R. , Kemp Deanna , Côte Claire , Arratia-Solar Andrea , Valenta Rick K. 
Published: September 2020

AbstractEnvironmental, social and governance pressures should feature in future scenario planning about the transition to a low carbon future. As low-carbon energy technologies advance, markets are driving demand for energy transition metals. Increased extraction rates will augment the stress placed on people and the environment in extractive locations. To quantify this stress, we develop a set of global composite environmental, social and governance indicators, and examine mining projects across 20 metal commodities to identify the co-occurrence of environmental, social and governance risk factors. Our findings show that 84% of platinum resources and 70% of cobalt resources are located in high-risk contexts. Reflecting heightened demand, major metals like iron and copper are set to disturb more land. Jurisdictions extracting energy transition metals in low-risk contexts are positioned to develop and maintain safeguards against mining-related social and environmental risk factors.
Constructing phase boundary in AgNbO3 antiferroelectrics: pathway simultaneously achieving high energy density and efficiency
Authors: Luo Nengneng , Han Kai , Cabral Matthew J. , Liao Xiaozhou , Zhang Shujun , Liao Changzhong , Zhang Guangzu , Chen Xiyong , Feng Qin , Li Jing-Feng , Wei Yuezhou 
Published: September 2020

AbstractDielectric capacitors with high energy storage density (Wrec) and efficiency (η) are in great demand for high/pulsed power electronic systems, but the state-of-the-art lead-free dielectric materials are facing the challenge of increasing one parameter at the cost of the other. Herein, we report that high Wrec of 6.3 J cm-3 with η of 90% can be simultaneously achieved by constructing a room temperature M2–M3 phase boundary in (1-x)AgNbO3-xAgTaO3 solid solution system. The designed material exhibits high energy storage stability over a wide temperature range of 20–150 °C and excellent cycling reliability up to 106 cycles. All these merits achieved in the studied solid solution are attributed to the unique relaxor antiferroelectric features relevant to the local structure heterogeneity and antiferroelectric ordering, being confirmed by scanning transmission electron microscopy and synchrotron X-ray diffraction. This work provides a good paradigm for developing new lead-free dielectrics for high-power energy storage applications.
Optoribogenetic control of regulatory RNA molecules
Authors: Pilsl Sebastian , Morgan Charles , Choukeife Moujab , Möglich Andreas , Mayer Günter 
Published: September 2020

AbstractShort regulatory RNA molecules underpin gene expression and govern cellular state and physiology. To establish an alternative layer of control over these processes, we generated chimeric regulatory RNAs that interact reversibly and light-dependently with the light-oxygen-voltage photoreceptor PAL. By harnessing this interaction, the function of micro RNAs (miRs) and short hairpin (sh) RNAs in mammalian cells can be regulated in a spatiotemporally precise manner. The underlying strategy is generic and can be adapted to near-arbitrary target sequences. Owing to full genetic encodability, it establishes optoribogenetic control of cell state and physiology. The method stands to facilitate the non-invasive, reversible and spatiotemporally resolved study of regulatory RNAs and protein function in cellular and organismal environments.
Purified Sika deer antler protein attenuates GM-induced nephrotoxicity by activating Nrf2 pathway and inhibiting NF-κB pathway
Authors: Wang Zhenyi , Wang Lulu , Wang Jing , Luo Jiacheng , Ruan Haonan , Zhang Jing 
Published: September 2020

AbstractAlthough gentamicin is widely used as an antibiotic in clinical practice, it also has some side-effects, such as acute kidney injury, which is a common condition caused by the abuse of gentamicin. Sika deer antler protein (SDAPR) can antagonize drug-induced AKI. Since SDAPR is recognized as an effective part of velvet antler, its components were further separated. Two components named SDAP1 and SDAP2 were obtained. The protective effects of SDAPR, SDAP1 and SDAP2 on GM-induced cytotoxicity to HEK293 and its potential mechanisms were studied. MTT and xCELLigence Real-Time cell analysis showed that SDAPR, SDAP1 and SDAP2 could protect HEK293 cells from GM toxicity. Similarly, SDAPR, SDAP1 and SDAP2 can reduce ROS level, reduce oxidative stress and improve inflammation Further studies have shown that SDAPR, SDAP1 and SDAP2 upregulate the Nrf2/HO-1 pathway by increasing the expression of Nrf2 and HO-1, and down-regulate the NF-κB pathway by reducing the protein expression of NF-κB. Annexin V/PI flow cytometry and Hoechst 33258 staining showed that SDAPR, SDAP1 and SDAP2 inhibited GM-induced apoptosis in HEK293 cells. Western blot analysis showed SDAPR, SDAP1 and SDAP2 decreased expression level of Bax and Cleaved-caspase-3, and increased the expression level of Bcl-2. In addition, we examined the feasibility of SDAP1 and SDAP1 to avoid kidney injury in a GM mouse model. In conclusion, SDAPR, SDAP1 and SDAP2 can be used to prevent GM-induced HEK293 cytotoxicity, probably because they have strong anti-oxidative stress, anti-inflammatory and anti-apoptotic effects. And SDAP1 and SDAP2 can inhibit GM-induced acute kidney injury in mice.
Design principles of gene evolution for niche adaptation through changes in protein–protein interaction networks
Authors: Carmi Gon , Tagore Somnath , Gorohovski Alessandro , Sivan Aviad , Raviv-Shay Dorith , Frenkel-Morgenstern Milana 
Published: September 2020

AbstractIn contrast to fossorial and above-ground organisms, subterranean species have adapted to the extreme stresses of living underground. We analyzed the predicted protein–protein interactions (PPIs) of all gene products, including those of stress-response genes, among nine subterranean, ten fossorial, and 13 aboveground species. We considered 10,314 unique orthologous protein families and constructed 5,879,879 PPIs in all organisms using ChiPPI. We found strong association between PPI network modulation and adaptation to specific habitats, noting that mutations in genes and changes in protein sequences were not linked directly with niche adaptation in the organisms sampled. Thus, orthologous hypoxia, heat-shock, and circadian clock proteins were found to cluster according to habitat, based on PPIs rather than on sequence similarities. Curiously, "ordered" domains were preserved in aboveground species, while "disordered" domains were conserved in subterranean organisms, and confirmed for proteins in DistProt database. Furthermore, proteins with disordered regions were found to adopt significantly less optimal codon usage in subterranean species than in fossorial and above-ground species. These findings reveal design principles of protein networks by means of alterations in protein domains, thus providing insight into deep mechanisms of evolutionary adaptation, generally, and particularly of species to underground living and other confined habitats.