bluuebunny/crossref_metadata_2025_split huggingface dataset:
The poly-SUMO2/3 protease SENP6 enables assembly of the constitutive centromere-associated network by group deSUMOylation
Authors: Liebelt Frauke , Jansen Nicolette S. , Kumar Sumit , Gracheva Ekaterina , Claessens Laura A. , Verlaan-de Vries Matty , Willemstein Edwin , Vertegaal Alfred C. O. 
Published: September 2019

AbstractIn contrast to our extensive knowledge on ubiquitin polymer signaling, we are severely limited in our understanding of poly-SUMO signaling. We set out to identify substrates conjugated to SUMO polymers, using knockdown of the poly-SUMO2/3 protease SENP6. We identify over 180 SENP6 regulated proteins that represent highly interconnected functional groups of proteins including the constitutive centromere-associated network (CCAN), the CENP-A loading factors Mis18BP1 and Mis18A and DNA damage response factors. Our results indicate a striking protein group de-modification by SENP6. SENP6 deficient cells are severely compromised for proliferation, accumulate in G2/M and frequently form micronuclei. Accumulation of CENP-T, CENP-W and CENP-A to centromeres is impaired in the absence of SENP6. Surprisingly, the increase of SUMO chains does not lead to ubiquitin-dependent proteasomal degradation of the CCAN subunits. Our results indicate that SUMO polymers can act in a proteolysis-independent manner and consequently, have a more diverse signaling function than previously expected.
Asymmetric catalysis mediated by a mirror symmetry-broken helical nanoribbon
Authors: Shen Zhaocun , Sang Yutao , Wang Tianyu , Jiang Jian , Meng Yan , Jiang Yuqian , Okuro Kou , Aida Takuzo , Liu Minghua 
Published: September 2019

AbstractAlthough chirality has been recognized as an essential entity for life, it still remains a big mystery how the homochirality in nature emerged in essential biomolecules. Certain achiral motifs are known to assemble into chiral nanostructures. In rare cases, their absolute geometries are enantiomerically biased by mirror symmetry breaking. Here we report the first example of asymmetric catalysis by using a mirror symmetry-broken helical nanoribbon as the ligand. We obtain this helical nanoribbon from a benzoic acid appended achiral benzene-1,3,5-tricarboxamide by its helical supramolecular assembly and employ it for the Cu2+-catalyzed Diels–Alder reaction. By thorough optimization of the reaction (conversion: > 99%, turnover number: ~90), the enantiomeric excess eventually reaches 46% (major/minor enantiomers = 73/27). We also confirm that the helical nanoribbon indeed carries helically twisted binding sites for Cu2+. Our achievement may provide the fundamental breakthrough for producing optically active molecules from a mixture of totally achiral motifs.
RBM3 promotes neurogenesis in a niche-dependent manner via IMP2-IGF2 signaling pathway after hypoxic-ischemic brain injury
Authors: Zhu Xinzhou , Yan Jingyi , Bregere Catherine , Zelmer Andrea , Goerne Tessa , Kapfhammer Josef P. , Guzman Raphael , Wellmann Sven 
Published: September 2019

AbstractHypoxic ischemia (HI) is an acute brain threat across all age groups. Therapeutic hypothermia ameliorates resulting injury in neonates but its side effects prevent routine use in adults. Hypothermia up-regulates a small protein subset that includes RNA-binding motif protein 3 (RBM3), which is neuroprotective under stressful conditions. Here we show how RBM3 stimulates neuronal differentiation and inhibits HI-induced apoptosis in the two areas of persistent adult neurogenesis, the subventricular zone (SVZ) and the subgranular zone (SGZ), while promoting neural stem/progenitor cell (NSPC) proliferation after HI injury only in the SGZ. RBM3 interacts with IGF2 mRNA binding protein 2 (IMP2), elevates its expression and thereby stimulates IGF2 release in SGZ but not SVZ-NSPCs. In summary, we describe niche-dependent regulation of neurogenesis after adult HI injury via the novel RBM3-IMP2-IGF2 signaling pathway.
Bacterially synthesized tellurium nanostructures for broadband ultrafast nonlinear optical applications
Authors: Wang Kangpeng , Zhang Xiaoyan , Kislyakov Ivan M. , Dong Ningning , Zhang Saifeng , Wang Gaozhong , Fan Jintai , Zou Xiao , Du Juan , Leng Yuxin , Zhao Quanzhong , Wu Kan , Chen Jianping , Baesman Shaun M. , Liao Kang-Shyang , Maharjan Surendra , Zhang Hongzhou , Zhang Long , Curran Seamus A. , Oremland Ronald S. , Blau Werner J. , Wang Jun 
Published: September 2019

AbstractElementary tellurium is currently of great interest as an element with potential promise in nano-technology applications because of the recent discovery regarding its three two-dimensional phases and the existence of Weyl nodes around its Femi level. Here, we report on the unique nano-photonic properties of elemental tellurium particles [Te(0)], as harvest from a culture of a tellurium-oxyanion respiring bacteria. The bacterially-formed nano-crystals prove effective in the photonic applications tested compared to the chemically-formed nano-materials, suggesting a unique and environmentally friendly route of synthesis. Nonlinear optical measurements of this material reveal the strong saturable absorption and nonlinear optical extinctions induced by Mie scattering over broad temporal and wavelength ranges. In both cases, Te-nanoparticles exhibit superior optical nonlinearity compared to graphene. We demonstrate that biological tellurium can be used for a variety of photonic applications which include their proof-of-concept for employment as ultrafast mode-lockers and all-optical switches.
The transcribed pseudogene RPSAP52 enhances the oncofetal HMGA2-IGF2BP2-RAS axis through LIN28B-dependent and independent let-7 inhibition
Authors: Oliveira-Mateos Cristina , Sánchez-Castillo Anaís , Soler Marta , Obiols-Guardia Aida , Piñeyro David , Boque-Sastre Raquel , Calleja-Cervantes Maria E. , Castro de Moura Manuel , Martínez-Cardús Anna , Rubio Teresa , Pelletier Joffrey , Martínez-Iniesta Maria , Herrero-Martín David , Tirado Oscar M. , Gentilella Antonio , Villanueva Alberto , Esteller Manel , Farré Lourdes , Guil Sonia 
Published: September 2019

AbstractOne largely unknown question in cell biology is the discrimination between inconsequential and functional transcriptional events with relevant regulatory functions. Here, we find that the oncofetalHMGA2gene is aberrantly reexpressed in many tumor types together with its antisense transcribed pseudogeneRPSAP52.RPSAP52is abundantly present in the cytoplasm, where it interacts with the RNA binding protein IGF2BP2/IMP2, facilitating its binding to mRNA targets, promoting their translation by mediating their recruitment on polysomes and enhancing proliferative and self-renewal pathways. Notably, downregulation ofRPSAP52impairs the balance between the oncogeneLIN28Band the tumor suppressorlet-7family of miRNAs, inhibits cellular proliferation and migration in vitro and slows down tumor growth in vivo. In addition, high levels ofRPSAP52in patient samples associate with a worse prognosis in sarcomas. Overall, we reveal the roles of a transcribed pseudogene that may display properties of an oncofetal master regulator in human cancers.
Activation of PKA via asymmetric allosteric coupling of structurally conserved cyclic nucleotide binding domains
Authors: Hao Yuxin , England Jeneffer P. , Bellucci Luca , Paci Emanuele , Hodges H. Courtney , Taylor Susan S. , Maillard Rodrigo A. 
Published: September 2019

AbstractCyclic nucleotide-binding (CNB) domains allosterically regulate the activity of proteins with diverse functions, but the mechanisms that enable the cyclic nucleotide-binding signal to regulate distant domains are not well understood. Here we use optical tweezers and molecular dynamics to dissect changes in folding energy landscape associated with cAMP-binding signals transduced between the two CNB domains of protein kinase A (PKA). We find that the response of the energy landscape upon cAMP binding is domain specific, resulting in unique but mutually coordinated tasks: one CNB domain initiates cAMP binding and cooperativity, whereas the other triggers inter-domain interactions that promote the active conformation. Inter-domain interactions occur in a stepwise manner, beginning in intermediate-liganded states between apo and cAMP-bound domains. Moreover, we identify a cAMP-responsive switch, the N3A motif, whose conformation and stability depend on cAMP occupancy. This switch serves as a signaling hub, amplifying cAMP-binding signals during PKA activation.
Direct evidence for grain boundary passivation in Cu(In,Ga)Se2 solar cells through alkali-fluoride post-deposition treatments
Authors: Nicoara Nicoleta , Manaligod Roby , Jackson Philip , Hariskos Dimitrios , Witte Wolfram , Sozzi Giovanna , Menozzi Roberto , Sadewasser Sascha 
Published: September 2019

AbstractThe properties and performance of polycrystalline materials depend critically on the properties of their grain boundaries. Polycrystalline photovoltaic materials – e.g. hybrid halide perovskites, copper indium gallium diselenide (CIGSe) and cadmium telluride – have already demonstrated high efficiencies and promise cost-effective electricity supply. For CIGSe-based solar cells, an efficiency above 23% has recently been achieved using an alkali-fluoride post-deposition treatment; however, its full impact and functional principle are not yet fully understood. Here, we show direct evidence for the passivation of grain boundaries in CIGSe treated with three different alkali-fluorides through a detailed study of the nanoscale optoelectronic properties. We determine a correlation of the surface potential change at grain boundaries with the open-circuit voltage, which is supported by numerical simulations. Our results suggest that heavier alkali elements might lead to better passivation by reducing the density of charged defects and increasing the formation of secondary phases at grain boundaries.
Proton-dynamic therapy following photosensitiser activation by accelerated protons demonstrated through fluorescence and singlet oxygen production
Authors: Grigalavicius M. , Mastrangelopoulou M. , Berg K. , Arous D. , Ménard M. , Raabe-Henriksen T. , Brondz E. , Siem S. , Görgen A. , Edin N. F. J. , Malinen E. , Theodossiou T. A. 
Published: September 2019

AbstractWe demonstrate excitation of photosensitisers (PSs) by accelerated protons to produce fluorescence and singlet oxygen. Their fluorescence follows a pattern similar to the proton energy loss in matter, while proton-derived fluorescence spectra match the photon-induced spectra. PSs excited in dry gelatin exhibit enhanced phosphorescence, suggesting an efficient PSs triplet state population. Singlet oxygen measurements, both optically at ~1270 nm and through the photoproduct of protoporphyrin IX (PpIX), demonstrate cytotoxic singlet oxygen generation by proton excitation. The singlet oxygen-specific scavenger 1,4-diazabicyclo[2.2.2]octane (DABCO) abrogates the photoproduct formation under proton excitation, but cannot countermand the overall loss of PpIX fluorescence. Furthermore, in two cell lines, M059K and T98G, we observe differential cell death upon the addition of the PS cercosporin, while in U87 cells we see no effect at any proton irradiation dose. Our results pave the way for a novel treatment combining proton therapy and “proton-dynamic therapy” for more efficient tumour eradication.
Mixing rate in Classical Many Body Systems
Authors: Frenkel Gad , Schwartz Moshe 
Published: September 2019

AbstractMixing in many body systems is intuitively understood as the change in time of the set of neighbors surrounding each particle. Its rate and its development over time hold important clues to the behavior of many body systems. For example, gas particles constantly change their position and surrounding particles, while in solids one expects the motion of the atoms to be limited by a fixed set of neighboring atoms. In other systems the situation is less clear. For example, agitated granular systems may behave like a fluid, a solid or glass, depending on various parameter such as density and friction. Thus, we introduce a parameter which describes the mixing rate in many body systems in terms of changes of a properly chosen adjacency matrix. The parameter is easily measurable in simulations but not in experiment. To demonstrate an application of the concept, we simulate a many body system, with particles interacting via a two-body potential and calculate the mixing rate as a function of time and volume fraction. The time dependence of the mixing rate clearly indicates the onset of crystallization
Inducing Mild Traumatic Brain Injury in C. elegans via Cavitation-Free Surface Acoustic Wave-Driven Ultrasonic Irradiation
Authors: Miansari Morteza , Mehta Meghna D. , Schilling Jan M. , Kurashina Yuta , Patel Hemal H. , Friend James 
Published: September 2019

AbstractMild traumatic brain injury is an all-too-common outcome from modern warfare and sport, and lacks a reproducible model for assessment of potential treatments and protection against it. Here we consider the use of surface acoustic wave (SAW) irradiation ofC.elegansworms—without cavitation—as a potential, ethically reasonable animal-on-a-chip model for inducing traumatic brain injury in an animal, producing significant effects on memory and learning that could prove useful in a model that progress from youth to old age in but a few weeks. We show a significant effect by SAW on the ability of worms to learn post-exposure through associative learning chemotaxis. At higher SAW intensity, we find immediate, thorough, but temporary paralysis of the worms. We further explore the importance of homogeneous exposure of the worms to the SAW-driven ultrasound, an aspect poorly controlled in past efforts, if at all, and demonstrate the absence of cavitation through a change in fluids from a standard media for the worms to the exceedingly viscous polyvinyl alcohol. Likewise, we demonstrate that acoustic streaming, when present, is not directly responsible for paralysis nor learning disabilities induced in the worm, but is beneficial at low amplitudes to ensuring homogeneous ultrasound exposure.
Different Grp94 components interact transiently with the myocilin olfactomedin domain in vitro to enhance or retard its amyloid aggregation
Authors: Huard Dustin J. E. , Jonke Alex P. , Torres Matthew P. , Lieberman Raquel L. 
Published: September 2019

AbstractThe inherited form of open angle glaucoma arises due to a toxic gain-of-function intracellular misfolding event involving a mutated myocilin olfactomedin domain (OLF). Mutant myocilin is recognized by the endoplasmic reticulum (ER)-resident heat shock protein 90 paralog, glucose regulated protein 94 (Grp94), but their co-aggregation precludes mutant myocilin clearance by ER-associated degradation. When the Grp94-mutant myocilin interaction is abrogated by inhibitors or siRNA, mutant myocilin is efficiently degraded. Here we dissected Grp94 into component domains (N, NM, MC) to better understand the molecular factors governing its interaction with OLF. We show that the Grp94 N-terminal nucleotide-binding N domain is responsible for accelerating OLF aggregation in vitro. Upon inhibiting the isolated N domain pharmacologically or removing the Pre-N terminal 57 residues from full-length Grp94, OLF aggregation rates revert to those seen for OLF alone, but only pharmacological inhibition rescues co-aggregation. The Grp94-OLF interaction is below the detection limit of fluorescence polarization measurements, but chemical crosslinking paired with mass spectrometry analyses traps a reproducible interaction between OLF and the Grp94 N domain, as well as between OLF and the Grp94 M domain. The emerging molecular-level picture of quinary interactions between Grp94 and myocilin points to a role for the far N-terminal sequence of the Grp94 N domain and a cleft in the M domain. Our work further supports drug discovery efforts to inhibit these interactions as a strategy to treat myocilin-associated glaucoma.
Agent-based modeling and bifurcation analysis reveal mechanisms of macrophage polarization and phenotype pattern distribution
Authors: Nickaeen Niloofar , Ghaisari Jafar , Heiner Monika , Moein Shiva , Gheisari Yousof 
Published: September 2019

AbstractMacrophages play a key role in tissue regeneration by polarizing to different destinies and generating various phenotypes. Recognizing the underlying mechanisms is critical in designing therapeutic procedures targeting macrophage fate determination. Here, to investigate the macrophage polarization, a nonlinear mathematical model is proposed in which the effect of IL4, IFNγ and LPS, as external stimuli, on STAT1, STAT6, and NFκB is studied using bifurcation analysis. The existence of saddle-node bifurcations in these internal key regulators allows different combinations of steady state levels which are attributable to different fates. Therefore, we propose dynamic bifurcation as a crucial built-in mechanism of macrophage polarization. Next, in order to investigate the polarization of a population of macrophages, bifurcation analysis is employed aligned with agent-based approach and a two-layer model is proposed in which the information from single cells is exploited to model the behavior in tissue level. Also, in this model, a partial differential equation describes the diffusion of secreted cytokines in the medium. Finally, the model was validated against a set of experimental data. Taken together, we have here developed a cell and tissue level model of macrophage polarization behavior which can be used for designing therapeutic interventions.
Effects of cultivation management on the winter wheat grain yield and water utilization efficiency
Authors: Wang Yonghua , Liu Huan , Huang Yuan , Wang Jinfeng , Wang Zhuangzhuang , Gu Fengxu , Xin Minghua , Kang Guozhang , Feng Wei , Guo Tiancai 
Published: September 2019

AbstractThe growth of winter wheat consumes a substantial amounts of water, and precipitation in most years cannot meet the water demand for the normal growth of winter wheat. The unsuitable irrigation strategies waste a large number of water resource, and the low water use efficiency has become the main factor limiting wheat yields. This research explored the effects of different cultivation managements on water consumption characteristics, water utilization efficiency, and grain yields of winter wheat. A field experiment, in which 4 cultivation managements including traditional cultivation management (T1), optimized cultivation management compared with T1 (T2), super high-yield cultivation management (T3) and optimized cultivation management compared with T3 (T4), was conducted during 2008–2010 to measure the above parameters. The results showed that different cultivation managements had significant effects on the total water consumption amounts and water source compositions. Total water consumption amounts in T1 and T3 managements were significantly higher than that in T2 and T4 managements, possibly from irrigation water. T2 and T4 managements remarkably increased the uptake and utilization of soil storage water and precipitation amounts. T3 and T1 managements increased and decreased water consumption in upper (0–40 cm) and lower (60–100 cm) soil layers, respectively, while effectively increased the consumption of storage water in middle and lower soil layers (60–100 cm) and yield water use efficiency (WUEY), precipitation water use efficiency (WUEP), soil water use efficiency (WUES), irrigation water use efficiency (WUEI), and irrigation efficiency (IE) in T4 and T2 managements were higher than those in T3 and T1, respectively. Total water consumption amounts markedly raised in T1 and T3 managements, whereas their soil storage water amounts utilization declined. T2 and T4 managements reduced irrigation water amounts and optimized the water and fertilizer supplies, resulting in significant increase in WUES and WUEI. Collectively, our results suggest that synergetic improving the water uptake and utilization of irrigation water and soil storage water can be the primary means to increase the grain yields and WUE.
Omnidirectional Light Capture by Solar Cells Mimicking the Structures of the Epidermal cells of Leaves
Authors: Yun Min Ju , Sim Yeon Hyang , Cha Seung I. , Lee Dong Yoon 
Published: September 2019

AbstractIt is important to develop solar cells that can capture and utilize omnidirectional light in urban environments, where photovoltaic (PV) devices are installed in fixed directions. We report a new design for such light capture, which mimics the structure of a leaf epidermis. First, we analyzed the epidermal structures of different plant species in detail so that we could copy them and fabricate light-trapping layers with different shapes: as lens arrays, pillars, and lens arrays with rough surfaces. Then we analyzed the results of two-dimensional ray-tracing simulations of perfectly aligned and Gaussian-scattered incident light in terms of light-trapping capabilities. Based on these results, we prepared high-performance dye-sensitized solar cells with light-trapping layers that exhibited omnidirectional light capturing functionality. Our layers enhanced the efficiency of obliquely incident light capture by 70%. Therefore, we expect that new possibilities for next-generation PVs, extending beyond the current rigid concepts, will arise upon the application of these results and from findings that build on these results.
Deep Learning for Semantic Segmentation of Defects in Advanced STEM Images of Steels
Authors: Roberts Graham , Haile Simon Y. , Sainju Rajat , Edwards Danny J. , Hutchinson Brian , Zhu Yuanyuan 
Published: September 2019

AbstractCrystalline materials exhibit long-range ordered lattice unit, within which resides nonperiodic structural features called defects. These crystallographic defects play a vital role in determining the physical and mechanical properties of a wide range of material systems. While computer vision has demonstrated success in recognizing feature patterns in images with well-defined contrast, automated identification of nanometer scale crystallographic defects in electron micrographs governed by complex contrast mechanisms is still a challenging task. Here, building upon an advanced defect imaging mode that offers high feature clarity, we introduce DefectSegNet - a new convolutional neural network (CNN) architecture that performs semantic segmentation of three common crystallographic defects in structural alloys: dislocation lines, precipitates and voids. Results from supervised training on a small set of high-quality defect images of steels show high pixel-wise accuracy across all three types of defects: 91.60 ± 1.77% on dislocations, 93.39 ± 1.00% on precipitates, and 98.85 ± 0.56% on voids. We discuss the sources of uncertainties in CNN prediction and the training data in terms of feature density, representation and homogeneity and their effects on deep learning performance. Further defect quantification using DefectSegNet prediction outperforms human expert average, presenting a promising new workflow for fast and statistically meaningful quantification of materials defects.