bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultrahigh-resolution nonlinear optical imaging of the armchair orientation in 2D transition metal dichalcogenides
Authors: Psilodimitrakopoulos Sotiris , Mouchliadis Leonidas , Paradisanos Ioannis , Lemonis Andreas , Kioseoglou George , Stratakis Emmanuel 
Published: May 2018

AbstractWe used nonlinear laser scanning optical microscopy to study atomically thin transition metal dichalcogenides (TMDs) and revealed, with unprecedented resolution, the orientational distribution of armchair directions and their degree of organization in the two-dimensional (2D) crystal lattice. In particular, we carried out polarization-resolved second-harmonic generation (PSHG) imaging for monolayer WS2 and obtained, with high-precision, the orientation of the main crystallographic axis (armchair orientation) for each individual 120 × 120 nm2 pixel of the 2D crystal area. Such nanoscale resolution was realized by fitting the experimental PSHG images, obtained with sub-micron precision, to a new generalized theoretical model that accounts for the nonlinear optical properties of TMDs. This enabled us to distinguish between different crystallographic domains, locate boundaries and reveal fine structure. As a consequence, we can calculate the mean orientational average of armchair angle distributions in specific regions of interest and define the corresponding standard deviation as a figure-of-merit for the 2D crystal quality.
Negative reflection and negative surface wave conversion from obliquely incident electromagnetic waves
Authors: Liu Shuo , Jun Cui Tie , Noor Ahsan , Tao Zui , Chi Zhang Hao , Dong Bai Guo , Yang Yan , Yang Zhou Xiao 
Published: May 2018

AbstractComplete control of spatially propagating waves (PWs) and surface waves (SWs) is an ultimate goal that scientists and engineers seek for, in which negative reflection of PW and negative surface wave are two exotic phenomena. Here, we experimentally demonstrate an anisotropic digital coding metasurface capable of controlling both PWs and SWs with a single coding pattern. On the basis of the digital description of coding metasurfaces, a simple coding method is proposed to allow dual functionalities (either PW or SW manipulations) under two orthogonal polarizations at arbitrarily oblique incidences, thus improving the adaptability of digital coding metasurfaces in more practical circumstances. With elaborately designed ellipse-shaped coding particles, we experimentally demonstrate various functions under oblique incidences, including the negative reflection of PW, negative SW, anomalous reflection and their arbitrary combinations, all having good agreements with theoretical and numerical predictions. We believe that the proposed method may enable the digital coding metasurfaces to have broad applications in radar detections, wireless communications and imaging.
Entanglement beating in free space through spin–orbit coupling
Authors: Otte Eileen , Rosales-Guzmán Carmelo , Ndagano Bienvenu , Denz Cornelia , Forbes Andrew 
Published: May 2018

AbstractIt is well known that the entanglement of a quantum state is invariant under local unitary transformations. This rule dictates, for example, that the entanglement of internal degrees of freedom of a photon remains invariant during free-space propagation. Here, we outline a scenario in which this paradigm does not hold. Using local Bell states engineered from classical vector vortex beams with non-separable degrees of freedom, the so-called classically entangled states, we demonstrate that the entanglement evolves during propagation, oscillating between maximally entangled (purely vector) and product states (purely scalar). We outline the spin–orbit interaction behind these novel propagation dynamics and confirm the results experimentally, demonstrating spin–orbit coupling in paraxial beams. This demonstration highlights a hitherto unnoticed property of classical entanglement and simultaneously offers a device for the on-demand delivery of vector states to targets, for example, for dynamic laser materials processing, switchable resolution within stimulated emission depletion (STED) systems, and a tractor beam for entanglement.
Sheathless inertial cell focusing and sorting with serial reverse wavy channel structures
Authors: Zhou Yinning , Ma Zhichao , Ai Ye 
Published: May 2018

AbstractInertial microfluidics utilizing passive hydrodynamic forces has been attracting significant attention in the field of precise microscale manipulation owing to its low cost, simplicity and high throughput. In this paper, we present a novel channel design with a series of reverse wavy channel structures for sheathless inertial particle focusing and cell sorting. A single wavy channel unit consists of four semicircular segments, which produce periodically reversed Dean secondary flow along the cross-section of the channel. The balance between the inertial lift force and the Dean drag force results in deterministic equilibrium focusing positions, which also depends on the size of the flow-through particles and cells. Six sizes of fluorescent microspheres (15, 10, 7, 5, 3 and 1 μm) were used to study the size-dependent inertial focusing behavior. Our novel design with sharp-turning subunits could effectively focus particles as small as 3 μm, the average size of platelets, enabling the sorting of cancer cells from whole blood without the use of sheath flows. Utilizing an optimized channel design, we demonstrated the size-based sorting of MCF-7 breast cancer cells spiked in diluted whole blood samples without using sheath flows. A single sorting process was able to recover 89.72% of MCF-7 cells from the original mixture and enrich MCF-7 cells from an original purity of 5.3% to 68.9% with excellent cell viability.
CARF enrichment promotes epithelial–mesenchymal transition via Wnt/β-catenin signaling: its clinical relevance and potential as a therapeutic target
Authors: Kalra Rajkumar S. , Chaudhary Anupama , Yoon A-Rum , Bhargava Priyanshu , Omar Amr , Garg Sukant , Yun Chae-Ok , Kaul Sunil C. , Wadhwa Renu 
Published: May 2018

AbstractCARF (Collaborator of ARF)/CDKN2AIP was discovered as a novel ARF-binding protein. It has been established as an essential cell survival, p53-, and cell proliferation-regulatory protein. Although a moderate upregulation of CARF caused growth arrest and senescence, its excessively enriched levels were shown to facilitate aggressive proliferation and malignant transformation of cancer cells. Here, we examined the relevance of CARF levels in clinical tumors and found its amplification (both at gene and transcript levels) in a variety of invasive and metastatic malignancies. Consistent with the clinical readouts, enrichment of CARF in cancer cells promoted epithelial–mesenchymal transition (EMT). Cancer database and molecular analyses revealed that it activates Wnt/β-catenin signaling axis, as evident by enhanced nuclear localization and function of β-catenin marked by increased level of SNAIL1, SNAIL2, ZEB1, and TWIST1 and its downstream gene targets. Of note, targeted knockdown of CARF led to decrease in nuclear β-catenin and its key downstream effectors, involved in EMT progression. Consistent with this, CARF targeting in vivo either by naked siRNA or CARF shRNA harboring adeno-oncolytic virus caused suppression of tumor progression and lung metastasis. Taken together, we report clinical and therapeutic relevance of CARF in EMT and cancer invasiveness/metastasis, and propose it as a potent therapeutic target of aggressive cancers.
Semaphorin 4D correlates with increased bone resorption, hypercalcemia, and disease stage in newly diagnosed patients with multiple myeloma
Authors: Terpos Evangelos , Ntanasis-Stathopoulos Ioannis , Christoulas Dimitrios , Bagratuni Tina , Bakogeorgos Marios , Gavriatopoulou Maria , Eleutherakis-Papaiakovou Evangelos , Kanellias Nikolaos , Kastritis Efstathios , Dimopoulos Meletios A. 
Published: May 2018

AbstractMultiple myeloma (MM) is characterized by bone destruction due to increased bone resorption and decreased bone formation. Semaphorin 4D (CD100, Sema4D) is expressed by osteoclasts, binds to its receptor Plexin-B1, and acts as a mediator of osteoclast–osteoblast interaction that ultimately inhibits osteoblastic bone formation. Preclinical data suggest that Sema4D/Plexin-B1 pathway is implicated in MM-induced bone disease. However, there is no information on the role of Sema4D in MM patients. Thus, we evaluated Sema4D and Plexin-B1 in six myeloma cells lines in vitro; in the bone marrow plasma (BMP) and serum of 72 newly diagnosed symptomatic MM (NDMM) patients and in 25 healthy controls. Only one myeloma cell line produced high Sema4D. BMP and circulating Sema4D and Plexin-B1 levels were significantly higher in MM patients compared to controls (p < 0.01). Sema4D correlated with serum calcium levels (p < 0.001), increased bone resorption (as assessed by CTX; p < 0.01), and ISS (p < 0.001). There was a trend for higher Sema4D levels in patients with osteolysis (p = 0.07), while patients with diffuse MRI pattern had higher BMP Sema4D levels (p = 0.02). Our data suggest that Sema4D is elevated in MM patients and correlate with adverse myeloma features and increased bone resorption, providing a possible target for novel therapeutic approaches in MM.
Genome-wide and high-density CRISPR-Cas9 screens identify point mutations in PARP1 causing PARP inhibitor resistance
Authors: Pettitt Stephen J. , Krastev Dragomir B. , Brandsma Inger , Dréan Amy , Song Feifei , Aleksandrov Radoslav , Harrell Maria I. , Menon Malini , Brough Rachel , Campbell James , Frankum Jessica , Ranes Michael , Pemberton Helen N. , Rafiq Rumana , Fenwick Kerry , Swain Amanda , Guettler Sebastian , Lee Jung-Min , Swisher Elizabeth M. , Stoynov Stoyno , Yusa Kosuke , Ashworth Alan , Lord Christopher J. 
Published: May 2018

AbstractAlthough PARP inhibitors (PARPi) target homologous recombination defective tumours, drug resistance frequently emerges, often via poorly understood mechanisms. Here, using genome-wide and high-density CRISPR-Cas9 “tag-mutate-enrich” mutagenesis screens, we identify close to full-length mutant forms of PARP1 that cause in vitro and in vivo PARPi resistance. Mutations both within and outside of the PARP1 DNA-binding zinc-finger domains cause PARPi resistance and alter PARP1 trapping, as does a PARP1 mutation found in a clinical case of PARPi resistance. This reinforces the importance of trapped PARP1 as a cytotoxic DNA lesion and suggests that PARP1 intramolecular interactions might influence PARPi-mediated cytotoxicity. PARP1 mutations are also tolerated in cells with a pathogenic BRCA1 mutation where they result in distinct sensitivities to chemotherapeutic drugs compared to other mechanisms of PARPi resistance (BRCA1 reversion, 53BP1, REV7 (MAD2L2) mutation), suggesting that the underlying mechanism of PARPi resistance that emerges could influence the success of subsequent therapies.
TGF-β induces miR-100 and miR-125b but blocks let-7a through LIN28B controlling PDAC progression
Authors: Ottaviani Silvia , Stebbing Justin , Frampton Adam E. , Zagorac Sladjana , Krell Jonathan , de Giorgio Alexander , Trabulo Sara M. , Nguyen Van T. M. , Magnani Luca , Feng Hugang , Giovannetti Elisa , Funel Niccola , Gress Thomas M. , Jiao Long R. , Lombardo Ylenia , Lemoine Nicholas R. , Heeschen Christopher , Castellano Leandro 
Published: May 2018

AbstractTGF-β/Activin induces epithelial-to-mesenchymal transition and stemness in pancreatic ductal adenocarcinoma (PDAC). However, the microRNAs (miRNAs) regulated during this response have remained yet undetermined. Here, we show that TGF-β transcriptionally induces MIR100HG lncRNA, containing miR-100, miR-125b and let-7a in its intron, via SMAD2/3. Interestingly, we find that although the pro-tumourigenic miR-100 and miR-125b accordingly increase, the amount of anti-tumourigenic let-7a is unchanged, as TGF-β also induces LIN28B inhibiting its maturation. Notably, we demonstrate that inactivation of miR-125b or miR-100 affects the TGF-β-mediated response indicating that these miRNAs are important TGF-β effectors. We integrate AGO2-RIP-seq with RNA-seq to identify the global regulation exerted by these miRNAs in PDAC cells. Transcripts targeted by miR-125b and miR-100 significantly overlap and mainly inhibit p53 and cell–cell junctions’ pathways. Together, we uncover that TGF-β induces an lncRNA, whose encoded miRNAs, miR-100, let-7a and miR-125b play opposing roles in controlling PDAC tumourigenesis.
Chiral Landau levels in Weyl semimetal NbAs with multiple topological carriers
Authors: Yuan Xiang , Yan Zhongbo , Song Chaoyu , Zhang Mengyao , Li Zhilin , Zhang Cheng , Liu Yanwen , Wang Weiyi , Zhao Minhao , Lin Zehao , Xie Tian , Ludwig Jonathan , Jiang Yuxuan , Zhang Xiaoxing , Shang Cui , Ye Zefang , Wang Jiaxiang , Chen Feng , Xia Zhengcai , Smirnov Dmitry , Chen Xiaolong , Wang Zhong , Yan Hugen , Xiu Faxian 
Published: May 2018

AbstractRecently, Weyl semimetals have been experimentally discovered in both inversion-symmetry-breaking and time-reversal-symmetry-breaking crystals. The non-trivial topology in Weyl semimetals can manifest itself with exotic phenomena, which have been extensively investigated by photoemission and transport measurements. Despite the numerous experimental efforts on Fermi arcs and chiral anomaly, the existence of unconventional zeroth Landau levels, as a unique hallmark of Weyl fermions, which is highly related to chiral anomaly, remains elusive owing to the stringent experimental requirements. Here, we report the magneto-optical study of Landau quantization in Weyl semimetal NbAs. High magnetic fields drive the system toward the quantum limit, which leads to the observation of zeroth chiral Landau levels in two inequivalent Weyl nodes. As compared to other Landau levels, the zeroth chiral Landau level exhibits a distinct linear dispersion in magnetic field direction and allows the optical transitions without the limitation of zero z momentum or $$\sqrt B$$

B

magnetic field evolution. The magnetic field dependence of the zeroth Landau levels further verifies the predicted particle-hole asymmetry of the Weyl cones. Meanwhile, the optical transitions from the normal Landau levels exhibit the coexistence of multiple carriers including an unexpected massive Dirac fermion, pointing to a more complex topological nature in inversion-symmetry-breaking Weyl semimetals. Our results provide insights into the Landau quantization of Weyl fermions and demonstrate an effective tool for studying complex topological systems.
Explaining the apparent impenetrable barrier to ultra-relativistic electrons in the outer Van Allen belt
Authors: Ozeke Louis G. , Mann Ian R. , Murphy Kyle R. , Degeling Alex W. , Claudepierre Seth G. , Spence Harlan E. 
Published: May 2018

AbstractRecent observations have shown the existence of an apparent impenetrable barrier at the inner edge of the ultra-relativistic outer electron radiation belt. This apparent impenetrable barrier has not been explained. However, recent studies have suggested that fast loss, such as associated with scattering into the atmosphere from man-made very-low frequency transmissions, is required to limit the Earthward extent of the belt. Here we show that the steep flux gradient at the implied barrier location is instead explained as a natural consequence of ultra-low frequency wave radial diffusion. Contrary to earlier claims, sharp boundaries in fast loss processes at the barrier are not needed. Moreover, we show that penetration to the barrier can occur on the timescale of days rather than years as previously reported, with the Earthward extent of the belt being limited by the finite duration of strong solar wind driving, which can encompass only a single geomagnetic storm.
The effects of mutational processes and selection on driver mutations across cancer types
Authors: Temko Daniel , Tomlinson Ian P. M. , Severini Simone , Schuster-Böckler Benjamin , Graham Trevor A. 
Published: May 2018

AbstractEpidemiological evidence has long associated environmental mutagens with increased cancer risk. However, links between specific mutation-causing processes and the acquisition of individual driver mutations have remained obscure. Here we have used public cancer sequencing data from 11,336 cancers of various types to infer the independent effects of mutation and selection on the set of driver mutations in a cancer type. First, we detect associations between a range of mutational processes, including those linked to smoking, ageing, APOBEC and DNA mismatch repair (MMR) and the presence of key driver mutations across cancer types. Second, we quantify differential selection between well-known alternative driver mutations, including differences in selection between distinct mutant residues in the same gene. These results show that while mutational processes have a large role in determining which driver mutations are present in a cancer, the role of selection frequently dominates.
Multidimensional heuristic process for high-yield production of astaxanthin and fragrance molecules in Escherichia coli
Authors: Zhang Congqiang , Seow Vui Yin , Chen Xixian , Too Heng-Phon 
Published: May 2018

AbstractOptimization of metabolic pathways consisting of large number of genes is challenging. Multivariate modular methods (MMMs) are currently available solutions, in which reduced regulatory complexities are achieved by grouping multiple genes into modules. However, these methods work well for balancing the inter-modules but not intra-modules. In addition, application of MMMs to the 15-step heterologous route of astaxanthin biosynthesis has met with limited success. Here, we expand the solution space of MMMs and develop a multidimensional heuristic process (MHP). MHP can simultaneously balance different modules by varying promoter strength and coordinating intra-module activities by using ribosome binding sites (RBSs) and enzyme variants. Consequently, MHP increases enantiopure 3S,3′S-astaxanthin production to 184 mg l−1 day−1 or 320 mg l−1. Similarly, MHP improves the yields of nerolidol and linalool. MHP may be useful for optimizing other complex biochemical pathways.
Regulatory protein SrpA controls phage infection and core cellular processes in Pseudomonas aeruginosa
Authors: You Jiajia , Sun Li , Yang Xiaojing , Pan Xuewei , Huang Zhiwei , Zhang Xixi , Gong Mengxin , Fan Zheng , Li Lingyan , Cui Xiaoli , Jing Zhaoyuan , Jin Shouguang , Rao Zhiming , Wu Weihui , Yang Hongjiang 
Published: May 2018

AbstractOur understanding of the molecular mechanisms behind bacteria-phage interactions remains limited. Here we report that a small protein, SrpA, controls core cellular processes in response to phage infection and environmental signals in Pseudomonas aeruginosa. We show that SrpA is essential for efficient genome replication of phage K5, and controls transcription by binding to a palindromic sequence upstream of the phage RNA polymerase gene. We identify potential SrpA-binding sites in 66 promoter regions across the P. aeruginosa genome, and experimentally validate direct binding of SrpA to some of these sites. Using transcriptomics and further experiments, we show that SrpA, directly or indirectly, regulates many cellular processes including cell motility, chemotaxis, biofilm formation, pyocyanin synthesis and protein secretion, as well as virulence in a Caenorhabditis elegans model of infection. Further research on SrpA and similar proteins, which are widely present in many other bacteria, is warranted.
Diffusion in translucent media
Authors: Shi Zhou , Genack Azriel Z. 
Published: May 2018

AbstractDiffusion is the result of repeated random scattering. It governs a wide range of phenomena from Brownian motion, to heat flow through window panes, neutron flux in fuel rods, dispersion of light in human tissue, and electronic conduction. It is universally acknowledged that the diffusion approach to describing wave transport fails in translucent samples thinner than the distance between scattering events such as are encountered in meteorology, astronomy, biomedicine, and communications. Here we show in optical measurements and numerical simulations that the scaling of transmission and the intensity profiles of transmission eigenchannels have the same form in translucent as in opaque media. Paradoxically, the similarities in transport across translucent and opaque samples explain the puzzling observations of suppressed optical and ultrasonic delay times relative to predictions of diffusion theory well into the diffusive regime.
Structural basis for cofilin binding and actin filament disassembly
Authors: Tanaka Kotaro , Takeda Shuichi , Mitsuoka Kaoru , Oda Toshiro , Kimura-Sakiyama Chieko , Maéda Yuichiro , Narita Akihiro 
Published: May 2018

AbstractActin depolymerizing factor (ADF) and cofilin accelerate actin dynamics by severing and disassembling actin filaments. Here, we present the 3.8 Å resolution cryo-EM structure of cofilactin (cofilin-decorated actin filament). The actin subunit structure of cofilactin (C-form) is distinct from those of F-actin (F-form) and monomeric actin (G-form). During the transition between these three conformations, the inner domain of actin (subdomains 3 and 4) and the majority of subdomain 1 move as two separate rigid bodies. The cofilin–actin interface consists of three distinct parts. Based on the rigid body movements of actin and the three cofilin–actin interfaces, we propose models for the cooperative binding of cofilin to actin, preferential binding of cofilin to ADP-bound actin filaments and cofilin-mediated severing of actin filaments.
Ultrafast probes of electron–hole transitions between two atomic layers
Authors: Wen Xiewen , Chen Hailong , Wu Tianmin , Yu Zhihao , Yang Qirong , Deng Jingwen , Liu Zhengtang , Guo Xin , Guan Jianxin , Zhang Xiang , Gong Yongji , Yuan Jiangtan , Zhang Zhuhua , Yi Chongyue , Guo Xuefeng , Ajayan Pulickel M. , Zhuang Wei , Liu Zhirong , Lou Jun , Zheng Junrong 
Published: May 2018

AbstractPhase transitions of electron–hole pairs on semiconductor/conductor interfaces determine fundamental properties of optoelectronics. To investigate interfacial dynamical transitions of charged quasiparticles, however, remains a grand challenge. By employing ultrafast mid-infrared microspectroscopic probes to detect excitonic internal quantum transitions and two-dimensional atomic device fabrications, we are able to directly monitor the interplay between free carriers and insulating interlayer excitons between two atomic layers. Our observations reveal unexpected ultrafast formation of tightly bound interlayer excitons between conducting graphene and semiconducting MoSe2. The result suggests carriers in the doped graphene are no longer massless, and an effective mass as small as one percent of free electron mass is sufficient to confine carriers within a 2D hetero space with energy 10 times larger than the room-temperature thermal energy. The interlayer excitons arise within 1 ps. Their formation effectively blocks charge recombination and improves charge separation efficiency for more than one order of magnitude.