bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elementary steps in electrical doping of organic semiconductors
Authors: Tietze Max L. , Benduhn Johannes , Pahner Paul , Nell Bernhard , Schwarze Martin , Kleemann Hans , Krammer Markus , Zojer Karin , Vandewal Koen , Leo Karl 
Published: March 2018

AbstractFermi level control by doping is established since decades in inorganic semiconductors and has been successfully introduced in organic semiconductors. Despite its commercial success in the multi-billion OLED display business, molecular doping is little understood, with its elementary steps controversially discussed and mostly-empirical-materials design. Particularly puzzling is the efficient carrier release, despite a presumably large Coulomb barrier. Here we quantitatively investigate doping as a two-step process, involving single-electron transfer from donor to acceptor molecules and subsequent dissociation of the ground-state integer-charge transfer complex (ICTC). We show that carrier release by ICTC dissociation has an activation energy of only a few tens of meV, despite a Coulomb binding of several 100 meV. We resolve this discrepancy by taking energetic disorder into account. The overall doping process is explained by an extended semiconductor model in which occupation of ICTCs causes the classically known reserve regime at device-relevant doping concentrations.
A bright organic NIR-II nanofluorophore for three-dimensional imaging into biological tissues
Authors: Wan Hao , Yue Jingying , Zhu Shoujun , Uno Takaaki , Zhang Xiaodong , Yang Qinglai , Yu Kuai , Hong Guosong , Wang Junying , Li Lulin , Ma Zhuoran , Gao Hongpeng , Zhong Yeteng , Su Jessica , Antaris Alexander L. , Xia Yan , Luo Jian , Liang Yongye , Dai Hongjie 
Published: March 2018

AbstractFluorescence imaging of biological systems in the second near-infrared (NIR-II, 1000–1700 nm) window has shown promise of high spatial resolution, low background, and deep tissue penetration owing to low autofluorescence and suppressed scattering of long wavelength photons. Here we develop a bright organic nanofluorophore (named p-FE) for high-performance biological imaging in the NIR-II window. The bright NIR-II >1100 nm fluorescence emission from p-FE affords non-invasive in vivo tracking of blood flow in mouse brain vessels. Excitingly, p-FE enables one-photon based, three-dimensional (3D) confocal imaging of vasculatures in fixed mouse brain tissue with a layer-by-layer imaging depth up to ~1.3 mm and sub-10 µm high spatial resolution. We also perform in vivo two-color fluorescence imaging in the NIR-II window by utilizing p-FE as a vasculature imaging agent emitting between 1100 and 1300 nm and single-walled carbon nanotubes (CNTs) emitting above 1500 nm to highlight tumors in mice.
RNA cytosine methylation and methyltransferases mediate chromatin organization and 5-azacytidine response and resistance in leukaemia
Authors: Cheng Jason X. , Chen Li , Li Yuan , Cloe Adam , Yue Ming , Wei Jiangbo , Watanabe Kenneth A. , Shammo Jamile M. , Anastasi John , Shen Qingxi J. , Larson Richard A. , He Chuan , Le Beau Michelle M. , Vardiman James W. 
Published: March 2018

AbstractThe roles of RNA 5-methylcytosine (RNA:m5C) and RNA:m5C methyltransferases (RCMTs) in lineage-associated chromatin organization and drug response/resistance are unclear. Here we demonstrate that the RCMTs, namely NSUN3 and DNMT2, directly bind hnRNPK, a conserved RNA-binding protein. hnRNPK interacts with the lineage-determining transcription factors (TFs), GATA1 and SPI1/PU.1, and with CDK9/P-TEFb to recruit RNA-polymerase-II at nascent RNA, leading to formation of 5-Azacitidine (5-AZA)-sensitive chromatin structure. In contrast, NSUN1 binds BRD4 and RNA-polymerase-II to form an active chromatin structure that is insensitive to 5-AZA, but hypersensitive to the BRD4 inhibitor JQ1 and to the downregulation of NSUN1 by siRNAs. Both 5-AZA-resistant leukaemia cell lines and clinically 5-AZA-resistant myelodysplastic syndrome and acute myeloid leukaemia specimens have a significant increase in RNA:m5C and NSUN1-/BRD4-associated active chromatin. This study reveals novel RNA:m5C/RCMT-mediated chromatin structures that modulate 5-AZA response/resistance in leukaemia cells, and hence provides a new insight into treatment of leukaemia.
Difluoromethylation of (hetero)aryl chlorides with chlorodifluoromethane catalyzed by nickel
Authors: Xu Chang , Guo Wen-Hao , He Xu , Guo Yin-Long , Zhang Xue-Ying , Zhang Xingang 
Published: March 2018

AbstractRelatively low reactivity hinders using chlorodifluoromethane (ClCF2H) for general difluoromethylation with organic molecules, despite its availability as an inexpensive industrial chemical. To date, transformations of ClCF2H are very limited and most of them involve difluorocarbene intermediate. Here, we describe a strategy for difluoromethylation of aromatics through nickel-catalyzed cross-coupling of ClCF2H with readily accessible (hetero)aryl chlorides. The reaction proceeds under mild reaction conditions with high efficiency and features synthetic simplicity without preformation of arylmetals and broad substrate scope, including a variety of heteroaromatics and commercially available pharmaceuticals. The reliable practicability and scalability of the current nickel-catalyzed process has also been demonstrated by several 10-g scale reactions without loss of reaction efficiency. Preliminary mechanistic studies reveal that the reaction starts from the oxidative addition of aryl chlorides to Ni(0) and a difluoromethyl radical is involved in the reaction, providing a route for applications of ClCF2H in organic synthesis and related chemistry.
Structure of Schlafen13 reveals a new class of tRNA/rRNA- targeting RNase engaged in translational control
Authors: Yang Jin-Yu , Deng Xiang-Yu , Li Yi-Sheng , Ma Xian-Cai , Feng Jian-Xiong , Yu Bing , Chen Yang , Luo Yi-Ling , Wang Xi , Chen Mei-Ling , Fang Zhi-Xin , Zheng Fu-Xiang , Li Yi-Ping , Zhong Qian , Kang Tie-Bang , Song Li-Bing , Xu Rui-Hua , Zeng Mu-Sheng , Chen Wei , Zhang Hui , Xie Wei , Gao Song 
Published: March 2018

AbstractCleavage of transfer (t)RNA and ribosomal (r)RNA are critical and conserved steps of translational control for cells to overcome varied environmental stresses. However, enzymes that are responsible for this event have not been fully identified in high eukaryotes. Here, we report a mammalian tRNA/rRNA-targeting endoribonuclease: SLFN13, a member of the Schlafen family. Structural study reveals a unique pseudo-dimeric U-pillow-shaped architecture of the SLFN13 N′-domain that may clamp base-paired RNAs. SLFN13 is able to digest tRNAs and rRNAs in vitro, and the endonucleolytic cleavage dissevers 11 nucleotides from the 3′-terminus of tRNA at the acceptor stem. The cytoplasmically localised SLFN13 inhibits protein synthesis in 293T cells. Moreover, SLFN13 restricts HIV replication in a nucleolytic activity-dependent manner. According to these observations, we term SLFN13 RNase S13. Our study provides insights into the modulation of translational machinery in high eukaryotes, and sheds light on the functional mechanisms of the Schlafen family.
Operando tribochemical formation of onion-like-carbon leads to macroscale superlubricity
Authors: Berman Diana , Narayanan Badri , Cherukara Mathew J. , Sankaranarayanan Subramanian K. R. S. , Erdemir Ali , Zinovev Alexander , Sumant Anirudha V. 
Published: March 2018

AbstractStress-induced reactions at the sliding interface during relative movement are known to cause structural or chemical modifications in contacting materials. The nature of these modifications at the atomic level and formation of byproducts in an oil-free environment, however, remain poorly understood and pose uncertainties in predicting the tribological performance of the complete tribosystem. Here, we demonstrate that tribochemical reactions occur even in dry conditions when hydrogenated diamond-like carbon (H-DLC) surface is slid against two-dimensional (2D) molybdenum disulfide along with nanodiamonds in dry nitrogen atmosphere. Detailed experimental studies coupled with reactive molecular dynamics simulations reveal that at high contact pressures, diffusion of sulfur from the dissociated molybdenum disulfide led to amorphization of nanodiamond and subsequent transformation to onion-like carbon structures (OLCs). The in situ formation of OLCs at the sliding interface provide reduced contact area as well as incommensurate contact with respect to the H-DLC surface, thus enabling successful demonstration of superlubricity
nc886 is induced by TGF-β and suppresses the microRNA pathway in ovarian cancer
Authors: Ahn Ji-Hye , Lee Hyun-Sung , Lee Ju-Seog , Lee Yeon-Su , Park Jong-Lyul , Kim Seon-Young , Hwang Jung-Ah , Kunkeaw Nawapol , Jung Sung Yun , Kim Tae Jin , Lee Kwang-Soo , Jeon Sung Ho , Lee Inhan , Johnson Betty H. , Choi Jung-Hye , Lee Yong Sun 
Published: March 2018

AbstractTransforming growth factor-β (TGF-β) signaling and microRNAs (miRNAs) are important gene regulatory components in cancer. Usually in advanced malignant stages, TGF-β signaling is elevated but global miRNA expression is suppressed. Such a gene expression signature is well illustrated in a fibrosis (or mesenchymal) subtype of ovarian cancer (OC) that is of poor prognosis. However, the interplay between the two pathways in the OC subtype has not yet been elucidated. nc886 is a recently identified non-coding RNA implicated in several malignancies. The high expression of nc886 is associated with poor prognosis in 285 OC patients. Herein, we find that in OC nc886 expression is induced by TGF-β and that nc886 binds to Dicer to inhibit miRNA maturation. By preventing the miRNA pathway, nc886 emulates TGF-β in gene expression patterns and potentiates cell adhesion, migration, invasion, and drug resistance. Here we report nc886 to be a molecular link between the TGF-β and miRNA pathways.
Adsorption-induced slip inhibition for polymer melts on ideal substrates
Authors: Ilton Mark , Salez Thomas , Fowler Paul D. , Rivetti Marco , Aly Mohammed , Benzaquen Michael , McGraw Joshua D. , Raphaël Elie , Dalnoki-Veress Kari , Bäumchen Oliver 
Published: March 2018

AbstractHydrodynamic slip, the motion of a liquid along a solid surface, represents a fundamental phenomenon in fluid dynamics that governs liquid transport at small scales. For polymeric liquids, de Gennes predicted that the Navier boundary condition together with polymer reptation implies extraordinarily large interfacial slip for entangled polymer melts on ideal surfaces; this Navier-de Gennes model was confirmed using dewetting experiments on ultra-smooth, low-energy substrates. Here, we use capillary leveling—surface tension driven flow of films with initially non-uniform thickness—of polymeric films on these same substrates. Measurement of the slip length from a robust one parameter fit to a lubrication model is achieved. We show that at the low shear rates involved in leveling experiments as compared to dewetting ones, the employed substrates can no longer be considered ideal. The data is instead consistent with a model that includes physical adsorption of polymer chains at the solid/liquid interface.
Bismuth and antimony-based oxyhalides and chalcohalides as potential optoelectronic materials
Authors: Ran Zhao , Wang Xinjiang , Li Yuwei , Yang Dongwen , Zhao Xin-Gang , Biswas Koushik , Singh David J. , Zhang Lijun 
Published: March 2018

AbstractIn the last decade the ns2 cations (e.g., Pb2+ and Sn2+)-based halides have emerged as one of the most exciting new classes of optoelectronic materials, as exemplified by for instance hybrid perovskite solar absorbers. These materials not only exhibit unprecedented performance in some cases, but they also appear to break new ground with their unexpected properties, such as extreme tolerance to defects. However, because of the relatively recent emergence of this class of materials, there remain many yet to be fully explored compounds. Here, we assess a series of bismuth/antimony oxyhalides and chalcohalides using consistent first principles methods to ascertain their properties and obtain trends. Based on these calculations, we identify a subset consisting of three types of compounds that may be promising as solar absorbers, transparent conductors, and radiation detectors. Their electronic structure, connection to the crystal geometry, and impact on band-edge dispersion and carrier effective mass are discussed.
Quantitative perfusion imaging of neoplastic liver lesions: A multi-institution study
Authors: Pahwa Shivani , Liu Hao , Chen Yong , Dastmalchian Sara , O’Connor Gregory , Lu Ziang , Badve Chaitra , Yu Alice , Wright Katherine , Chalian Hamid , Rao Shengxiang , Fu Caixia , Vallines Ignacio , Griswold Mark , Seiberlich Nicole , Zeng Mengsu , Gulani Vikas 
Published: March 2018

AbstractWe describe multi-institutional experience using free-breathing, 3D Spiral GRAPPA-based quantitative perfusion MRI in characterizing neoplastic liver masses. 45 patients (age: 48–72 years) were prospectively recruited at University Hospitals, Cleveland, USA on a 3 Tesla (T) MRI, and at Zhongshan Hospital, Shanghai, China on a 1.5 T MRI. Contrast-enhanced volumetric T1-weighted images were acquired and a dual-input single-compartment model used to derive arterial fraction (AF), distribution volume (DV) and mean transit time (MTT) for the lesions and normal parenchyma. The measurements were compared using two-tailed Student’s t-test, with Bonferroni correction applied for multiple-comparison testing. 28 hepatocellular carcinoma (HCC) and 17 metastatic lesions were evaluated. No significant difference was noted in perfusion parameters of normal liver parenchyma and neoplastic masses at two centers (p = 0.62 for AF, 0.015 for DV, 0.42 for MTT for HCC, p = 0.13 for AF, 0.97 for DV, 0.78 for MTT for metastases). There was statistically significant difference in AF, DV, and MTT of metastases and AF and DV of HCC compared to normal liver parenchyma (p < 0.5/9 = 0.0055). A statistically significant difference was noted in the MTT of metastases compared to hepatocellular carcinoma (p < 0.001*10-5). In conclusion, 3D Spiral-GRAPPA enabled quantitative free-breathing perfusion MRI exam provides robust perfusion parameters.
Dual role of E-cadherin in the regulation of invasive collective migration of mammary carcinoma cells
Authors: Elisha Yair , Kalchenko Vyacheslav , Kuznetsov Yuri , Geiger Benjamin 
Published: March 2018

AbstractIn this article, we explore a non-canonical form of collective cell migration, displayed by the metastatic murine mammary carcinoma cell line 4T1. We show here that in sparsely plated 4T1 cells, E-cadherin levels are moderately reduced (~50%), leading to the development of collective migration, whereby cells translocate in loose clusters, interconnected by thin membrane tethers. Knocking down E-cadherin blocked tether formation in these cells, leading to enhancement of migration rate and, at the same time, to suppression of lung metastases formation in vivo, and inhibition of infiltration into fibroblast monolayers ex vivo. These findings suggest that the moderate E-cadherin levels present in wild-type 4T1 cells play a key role in promoting cancer invasion and metastasis.
Virulence factors of Moraxella catarrhalis outer membrane vesicles are major targets for cross-reactive antibodies and have adapted during evolution
Authors: Augustyniak Daria , Seredyński Rafał , McClean Siobhán , Roszkowiak Justyna , Roszniowski Bartosz , Smith Darren L. , Drulis-Kawa Zuzanna , Mackiewicz Paweł 
Published: March 2018

AbstractMoraxella catarrhalis is a common human respiratory tract pathogen. Its virulence factors associated with whole bacteria or outer membrane vesicles (OMVs) aid infection, colonization and may induce specific antibodies. To investigate pathogen-host interactions, we applied integrated bioinformatic and immunoproteomic (2D-electrophoresis, immunoblotting, LC-MS/MS) approaches. We showed that OMV proteins engaged exclusively in complement evasion and colonization strategies, but not those involved in iron transport and metabolism, are major targets for cross-reacting antibodies produced against phylogenetically divergent M. catarrhalis strains. The analysis of 31 complete genomes of M. catarrhalis and other Moraxella revealed that OMV protein-coding genes belong to 64 orthologous groups, five of which are restricted to M. catarrhalis. This species showed a two-fold increase in the number of OMV protein-coding genes relative to its ancestors and animal-pathogenic Moraxella. The appearance of specific OMV factors and the increase in OMV-associated virulence proteins during M. catarrhalis evolution is an interesting example of pathogen adaptation to optimize colonization. This precisely targeted cross-reactive immunity against M. catarrhalis may be an important strategy of host defences to counteract this phenomenon. We demonstrate that cross-reactivity is closely associated with the anti-virulent antibody repertoire which we have linked with adaptation of this pathogen to the host.
Intermittent dynamics in complex systems driven to depletion
Authors: Escobar Juan V. , Pérez Castillo Isaac 
Published: March 2018

AbstractWhen complex systems are driven to depletion by some external factor, their non-stationary dynamics can present an intermittent behaviour between relative tranquility and burst of activity whose consequences are often catastrophic. To understand and ultimately be able to predict such dynamics, we propose an underlying mechanism based on sharp thresholds of a local generalized energy density that naturally leads to negative feedback. We find a transition from a continuous regime to an intermittent one, in which avalanches can be predicted despite the stochastic nature of the process. This model may have applications in many natural and social complex systems where a rapid depletion of resources or generalized energy drives the dynamics. In particular, we show how this model accurately describes the time evolution and avalanches present in a real social system.
A Comprehensive Physical Impedance Model of Polymer Electrolyte Fuel Cell Cathodes in Oxygen-free Atmosphere
Authors: Obermaier Michael , Bandarenka Aliaksandr S. , Lohri-Tymozhynsky Cyrill 
Published: March 2018

AbstractElectrochemical impedance spectroscopy (EIS) is an indispensable tool for non-destructive operando characterization of Polymer Electrolyte Fuel Cells (PEFCs). However, in order to interpret the PEFC’s impedance response and understand the phenomena revealed by EIS, numerous semi-empirical or purely empirical models are used. In this work, a relatively simple model for PEFC cathode catalyst layers in absence of oxygen has been developed, where all the equivalent circuit parameters have an entire physical meaning. It is based on: (i) experimental quantification of the catalyst layer pore radii, (ii) application of De Levie’s analytical formula to calculate the response of a single pore, (iii) approximating the ionomer distribution within every pore, (iv) accounting for the specific adsorption of sulfonate groups and (v) accounting for a small H2crossover through ~15 μm ionomer membranes. The derived model has effectively only 6 independent fitting parameters and each of them has clear physical meaning. It was used to investigate the cathode catalyst layer and the double layer capacitance at the interface between the ionomer/membrane and Pt-electrocatalyst. The model has demonstrated excellent results in fitting and interpretation of the impedance data under different relative humidities. A simple script enabling fitting of impedance data is provided as supporting information.
Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms
Authors: Rastogi Achal , Maheswari Uma , Dorrell Richard G. , Vieira Fabio Rocha Jimenez , Maumus Florian , Kustka Adam , McCarthy James , Allen Andy E. , Kersey Paul , Bowler Chris , Tirichine Leila 
Published: March 2018

AbstractDiatoms are one of the most successful and ecologically important groups of eukaryotic phytoplankton in the modern ocean. Deciphering their genomes is a key step towards better understanding of their biological innovations, evolutionary origins, and ecological underpinnings. Here, we have used 90 RNA-Seq datasets from different growth conditions combined with published expressed sequence tags and protein sequences from multiple taxa to explore the genome of the model diatom Phaeodactylum tricornutum, and introduce 1,489 novel genes. The new annotation additionally permitted the discovery of extensive alternative splicing in diatoms, including intron retention and exon skipping, which increase the diversity of transcripts generated in changing environments. In addition, we have used up-to-date reference sequence libraries to dissect the taxonomic origins of diatom genes. We show that the P. tricornutum genome is enriched in lineage-specific genes, with up to 47% of the gene models present only possessing orthologues in other stramenopile groups. Finally, we have performed a comprehensive de novo annotation of repetitive elements showing novel classes of transposable elements such as SINE, MITE and TRIM/LARD. This work provides a solid foundation for future studies of diatom gene function, evolution and ecology.
The evolutionarily conserved genes: Tex37, Ccdc73, Prss55 and Nxt2 are dispensable for fertility in mice
Authors: Khan Manan , Jabeen Nazish , Khan Teka , Hussain Hafiz Muhammad Jafar , Ali Asim , Khan Ranjha , Jiang Long , Li Tao , Tao Qizhao , Zhang Xingxia , Yin Hao , Yu Changping , Jiang Xiaohua , Shi Qinghua 
Published: March 2018

AbstractThere are more than 2300 genes that are predominantly expressed in mouse testes. The role of hundreds of these genes has been studied in mouse spermatogenesis but still there are many genes whose function is unknown. Gene knockout (KO) strategy in mice is widely used for in vivo study of gene function. The present study was designed to explore the function of the four genes: Tex37, Ccdc73, Prss55 and Nxt2, which were evolutionarily conserved in eutherians. We found that these genes had a testis-enriched expression pattern in mice except Nxt2. We knocked out these genes by CRISPR/Cas9 individually and found that all the KO mice had normal fertility with no detectable difference in testis/body weight ratios, epididymal sperm counts, as well as testicular and epididymal histology from wild type mice. Although these genes are evolutionarily conserved in eutherians including human and mouse, they are not individually essential for spermatogenesis, testis development and male fertility in mice in laboratory conditions. Our report of these fertile KO data could avoid the repetition and duplication of efforts which will help in prioritizing efforts to focus on genes that are indispensable for male reproduction.