bluuebunny/crossref_metadata_2025 huggingface dataset:
Measuring the Stellar Halo Velocity Anisotropy With 3D Kinematics
Authors: Cunningham Emily C. , Deason Alis J. , Guhathakurta Puragra , Rockosi Constance M. , van der Marel Roeland P. , Sohn S. Tony
Published: May 2016

We present the first measurement of the anisotropy parameter β using 3D kinematic information outside of the solar neighborhood. Our sample consists of 13 Milky Way halo stars with measured proper motions and radial velocities in the line of sight of M31. Proper motions were measured using deep, multi-epoch HST imaging, and radial velocities were measured from Keck II/DEIMOS spectra. We measure β = −0.3−0.9+0.4, which is consistent with isotropy, and inconsistent with measurements in the solar neighborhood. We suggest that this may be the kinematic signature of a relatively early, massive accretion event, or perhaps several such events.
The early gaseous and stellar mass assembly of Milky Way-type galaxy halos
Authors: Hensler Gerhard , Petrov Mykola
Published: May 2016

How the Milky Way has accumulated its mass over the Hubble time, whether significant amounts of gas and stars were accreted from satellite galaxies, or whether the Milky Way has experienced an initial gas assembly and then evolved more-or-less in isolation is one of the burning questions in modern astronomy, because it has consequences for our understanding of galaxy formation in the cosmological context. Here we present the evolutionary model of a Milky Way-type satellite system zoomed into a cosmological large-scale simulation. Embedded into Dark Matter halos and allowing for baryonic processes these chemo-dynamical simulations aim at studying the gas and stellar loss from the satellites to feed the Milky Way halo and the stellar chemical abundances in the halo and the satellite galaxies.
Chemical evolution of r-process elements in the Draco dwarf spheroidal galaxy
Authors: Ishigaki M. N. , Tsujimoto T. , Shigeyama T. , Aoki W.
Published: May 2016

A dominant astrophysical site for r-process, which is responsible for producing heavy neutron-capture elements, is unknown. Dwarf spheroidal galaxies around the Milky Way halo provide ideal laboratories to investigate the origin and evolution of r-process elements. We carried out high-resolution spectroscopic observations of three giant stars in the Draco dwarf spheroidal galaxy to estimate their europium abundances. We found that the upper-limits of [Eu/H] are very low in the range [Fe/H] < −2, while this ratio is nearly constant at higher metallicities. This trend is not well reproduced with models which assume that Eu is produced together with Fe by SNe, and may suggest the contribution from other objects such as neutron-star mergers.
Very Low-Mass Stars with Extremely Low Metallicity in the Milky Way's Halo
Authors: Aoki Wako , Beers Timothy C. , Suda Takuma , Honda Satoshi , Lee Young Sun
Published: May 2016

Large surveys and follow-up spectroscopic studies in the past few decades have been providing chemical abundance data for a growing number of very metal-poor ([Fe/H] <−2) stars. Most of them are red giants or main-sequence turn-off stars having masses near 0.8 solar masses. Lower mass stars with extremely low metallicity ([Fe/H] <−3) are yet to be explored. Our high-resolution spectroscopic study for very metal-poor stars found with SDSS has identified four cool main-sequence stars with [Fe/H] <−2.5 among 137 objects (Aoki et al. 2013). The effective temperatures of these stars are 4500–5000 K, corresponding to a mass of around 0.5 solar masses. Our standard analysis of the high-resolution spectra based on 1D-LTE model atmospheres has obtained self-consistent chemical abundances for these objects, assuming small values of micro-turbulent velocities compared with giants and turn-off stars. The low temperature of the atmospheres of these objects enables us to measure their detailed chemical abundances. Interestingly, two of the four stars have extreme chemical-abundance patterns: one has the largest excesses of heavy neutron-capture elements associated with the r-process abundance pattern known to date (Aoki et al. 2010), and the other exhibits low abundances of the α-elements and odd-Z elements, suggested to be signatures of the yields of very massive stars (> 100 solar masses; Aoki et al. 2014). Although the sample size is still small, these results indicate the potential of very low-mass stars as probes to study the early stages of the Milky Way's halo formation.
Measure the local dark matter density with LAMOST spectroscopic survey
Authors: Liu Chao , Xia Qiran , Mao Shude
Published: May 2016

The local dark matter density plays the key role in the distribution of the dark matter halo near the Galactic disk. It will also answer whether a dark matter disk exists in the Milky Way. We measure the local dark matter density with LAMOST observed stars located at around the north Galactic pole. The selection effects of the observations are well considered and corrected. We find that the derived DM density, which is around 0.0159+0.0047−0.0057M⊙ pc−3 providing a flat local rotation curve.
RR Lyrae to understand the Galactic halo
Authors: Fiorentino Giuliana
Published: May 2016

We present recent results obtained using old variable RR Lyrae stars on the Galactic halo structure and its connection with nearby dwarf galaxies. We compare the period and period-amplitude distributions for a sizeable sample of fundamental mode RR Lyrae stars (RRab) in dwarf spheroidals (~1300 stars) with those in the Galactic halo (~16'000 stars) and globular clusters (~1000 stars). RRab in dwarfs –as observed today– do not appear to follow the pulsation properties shown by those in the Galactic halo, nor they have the same properties as RRab in globulars. Thanks to the OGLE experiment we extended our comparison to massive metal–rich satellites like the dwarf irregular Large Magellanic Cloud (LMC) and the Sagittarius (Sgr) dwarf spheroidal. These massive and more metal–rich stellar systems likely have contributed to the Galactic halo formation more than classical dwarf spheroidals.

Finally, exploiting the intrinsic nature of RR Lyrae as distance indicators we were able to study the period and period amplitude distributions of RRab within the Halo. It turned out that the inner and the outer Halo do show a difference that may suggest a different formation scenario (in situ vs accreted).
The Outer Galactic Halo As Probed By RR Lyr Stars From the Palomar Transient Facility + Keck
Authors: Cohen Judith , Sesar Branimir , Banholzer Sophianna ,   the PTF Collaboration
Published: May 2016

We present initial results from our study of the outer halo of the Milky Way using a large sample of RR Lyr(ab) variables datamined from the archives of the Palomar Transient Facility. Of the 464 RR Lyr in our sample with distances exceeding 50 kpc, 62 have been observed spectroscopically at the Keck Observatory. vr and σ(vr) are given as a function of distance between 50 and 110 kpc, and a very preliminary rather low total mass for the Milky Way out to 110 kpc of ~7±1.5×1011M⊙ is derived from our data.
Reconstructing the Accretion History of the Galactic Halo Using Stellar Chemical Abundance Ratio Distributions
Authors: Lee Duane M. , Johnston Kathryn V. , Sen Bodhisattva , Jessop Will
Published: May 2016

In this study we tested the prospects of using 2D chemical abundance ratio distributions (CARDs) found in stars of the stellar halo to determine its formation history. First, we used simulated data from eleven “MW-like” halos to generate satellite template sets of 2D CARDs of accreted dwarf satellites which are comprised of accreted dwarfs from various mass regimes and epochs of accretion. Next, we randomly drew samples of ~ 103–4 mock observations of stellar chemical abundance ratios ([α/Fe], [Fe/H]) from those eleven halos to generate samples of the underlying densities for our CARDs to be compared to our templates in our analysis. Finally, we used the expectation-maximization algorithm to derive accretion histories in relation to the satellite template set (STS) used and the sample size. For certain STS used we typically can identify the relative mass contributions of all accreted satellites to within a factor of 2. We also find that this method is particularly sensitive to older accretion events involving low-luminous dwarfs e.g. ultra-faint dwarfs — precisely those events that are too ancient to be seen by phase-space studies of stars and too faint to be seen by high-z studies of the early Universe. Since our results only exploit two chemical dimensions and near-future surveys promise to provide ~ 6–9 dimensions, we conclude that these new high-resolution spectroscopic surveys of the stellar halo will allow us (given the development of new CARD–generating dwarf models) to recover the luminosity function of infalling dwarf galaxies — and the detailed accretion history of the halo — across cosmic time.
The formation of the smooth halo component
Authors: Peñarrubia Jorge
Published: May 2016

The detection and characterization of debris in the integral-of-motion space is a promising avenue to uncover the hierarchical formation of the Milky Way. Yet, the fact that the integrals do not remain constant during the assembly process adds considerable complexity to this approach. Indeed, in time-dependent potentials tidal substructures tend to be effaced from the integral-of-motion space through an orbital diffusion process, which naturally leads to the formation of a ‘smooth’ stellar halo. In this talk I will introduce a new probability theory that describes the evolution of collisionless systems subject to a time-dependent potential. The new theory can be used to reconstruct the hierarchical assembly of our Galaxy through modelling the observed distribution of accreted stars in the integral-of-motion space.
Subjektive Geschlechtstyp- und Prestigeeinschätzungen
Authors: Steinritz Gaby , Lehmann-Grube Sabine K. , Ziegler Birgit
Published: May 2016

Zusammenfassung. Zur Überprüfung von Gottfredsons Theorie der entwicklungsbedingten Eingrenzung beruflicher Aspirationen wurden Geschlechtstyp- und Prestigeeinschätzungen von Berufen bei insgesamt n = 959 Jugendlichen erhoben. Im Unterschied zur gängigen Abfrage von Wunschberufen im freien Antwortformat wurden die Wunschberufe der Jugendlichen über Einschätzungslisten erfasst. Die Ergebnisse zeigen signifikante Unterschiede nach Geschlecht und Klassenstufe. Weibliche Jugendliche bilden ein größeres berufliches Aspirationsfeld. Zum einen zeigen sie eine größere Akzeptanzspanne auf der Geschlechtsdimension, zum anderen ein niedrigeres Mindestniveau auf der Prestigedimension. Für die Diagnostik und Berufsberatung legen die Ergebnisse nahe, neben manifesten Interessen sich früh herausbildende Berufsorientierungen und Geschlechtsunterschiede in der Begrenzung beruflicher Aspirationen in den Blick zu nehmen.
New Developments in the Assessment of Vocational Interests and Implications for Research and Practice
Authors: Hell Benedikt , Wille Bart , Höft Stefan
Published: May 2016

Abstract. The assessment and research of vocational interests have a long history in psychology. Our bibliometric analysis shows a steep rise in publication numbers focused on vocational interests immediately after John Holland’s (1959) seminal work and a newly awakened impetus especially in German-speaking countries since the 1990’s. Contemporary research focuses on new structural models of vocational interests and attempts to further consolidate the construct validity of interests by delving deeper into the associations with personality and cognitive abilities. The enormous research activity of the past couple of decades culminated in two meta-analyses on the criterion-related validity of vocational interests, which reveal moderate validities with respect to occupational criteria, yet sophisticated matching algorithms and more detailed interest models raise expectations for a more precise prediction. The studies included in this special issue contribute to this vivid field of research by (1) rethinking the relationship between creative and investigative interests in particular and the Big Five personality traits, (2) analyzing the interlink between secondary vocational interest constructs and several indicators of career preparedness, (3) testing Gottfredson’s developmental theory of occupational aspirations, and (4) investigating the perceived benefits of online self-assessments in an experimental pretest-posttest control group design.
Superior visible light hydrogen evolution of Janus bilayer junctions via atomic-level charge flow steering
Authors: Li Jie , Zhan Guangming , Yu Ying , Zhang Lizhi
Published: May 2016

Although photocatalytic hydrogen evolution (PHE) is ideal for solar-to-fuel conversion, it remains challenging to construct a highly efficient PHE system by steering the charge flow in a precise manner. Here we tackle this challenge by assembling 1T MoS2 monolayers selectively and chemically onto (Bi12O17) end-faces of Bi12O17Cl2 monolayers to craft two-dimensional (2D) Janus (Cl2)-(Bi12O17)-(MoS2) bilayer junctions, a new 2D motif different from van der Waals heterostructure. Electrons and holes from visible light-irradiated Bi12O17Cl2 are directionally separated by the internal electric field to (Bi12O17) and (Cl2) end-faces, respectively. The separated electrons can further migrate to MoS2 via Bi–S bonds formed between (Bi12O17) and MoS2 monolayers. This atomic-level directional charge separation endows the Janus bilayers with ultralong carrier lifetime of 3,446 ns and hence a superior visible-light PHE rate of 33 mmol h−1 g−1. Our delineated Janus bilayer junctions on the basis of the oriented assembly of monolayers presents a new design concept to effectively steer the charge flow for PHE.
Sampling the structure and chemical order in assemblies of ferromagnetic nanoparticles by nuclear magnetic resonance
Authors: Liu Yuefeng , Luo Jingjie , Shin Yooleemi , Moldovan Simona , Ersen Ovidiu , Hébraud Anne , Schlatter Guy , Pham-Huu Cuong , Meny Christian
Published: May 2016

Assemblies of nanoparticles are studied in many research fields from physics to medicine. However, as it is often difficult to produce mono-dispersed particles, investigating the key parameters enhancing their efficiency is blurred by wide size distributions. Indeed, near-field methods analyse a part of the sample that might not be representative of the full size distribution and macroscopic methods give average information including all particle sizes. Here, we introduce temperature differential ferromagnetic nuclear resonance spectra that allow sampling the crystallographic structure, the chemical composition and the chemical order of non-interacting ferromagnetic nanoparticles for specific size ranges within their size distribution. The method is applied to cobalt nanoparticles for catalysis and allows extracting the size effect from the crystallographic structure effect on their catalytic activity. It also allows sampling of the chemical composition and chemical order within the size distribution of alloyed nanoparticles and can thus be useful in many research fields.
Extracellular and intracellular cleavages of proBDNF required at two distinct stages of late-phase LTP
Authors: Pang Petti T , Nagappan Guhan , Guo Wei , Lu Bai
Published: May 2016

Although late-phase long-term potentiation (L-LTP) is implicated in long-term memory, its molecular mechanisms are largely unknown. Here we provide evidence that L-LTP can be divided into two stages: an induction stage (I) and a maintenance stage (II). Both stages require mature brain-derived neurotrophic factor (mBDNF), but involve distinct underlying mechanisms. Stage I requires secretion of existing proBDNF followed by extracellular cleavage by tPA/plasmin. Stage II depends on newly synthesized BDNF. Surprisingly, mBDNF at stage II is derived from intracellular cleavage of proBDNF by furin/PC1. Moreover, stage I involves BDNF-TrkB signaling mainly through MAP kinase, whereas all three signaling pathways (phospholipase C-γ, PI3 kinase, and MAP kinase) are required for the maintenance of L-LTP at stage II. These results reveal the molecular basis for two temporally distinct stages in L-LTP, and provide insights on how BDNF modulates this long-lasting synaptic alternation at two critical time windows.
Association of p53 codon72 Arg>Pro polymorphism with susceptibility to nasopharyngeal carcinoma: evidence from a case–control study and meta-analysis
Authors: Sahu S K , Chakrabarti S , Roy S D , Baishya N , Reddy R R , Suklabaidya S , Kumar A , Mohanty S , Maji S , Suryanwanshi A , Rajasubramaniam S , Asthana M , Panda A K , Singh S P , Ganguly S , Shaw O P , Bichhwalia A K , Sahoo P K , Chattopadhyay N R , Chatterjee K , Kundu C N , Das A K , Kannan R , Zorenpuii  , Zomawia E , Sema S A , Singh Y I , Ghosh S K , Sharma K , Das B S , Choudhuri T
Published: May 2016

Tumor suppressor p53 is a critical player in the fight against cancer as it controls the cell cycle check point, apoptotic pathways and genomic stability. It is known to be the most frequently mutated gene in a wide variety of human cancers. Single-nucleotide polymorphism of p53 at codon72 leading to substitution of proline (Pro) in place of arginine (Arg) has been identified as a risk factor for development of many cancers, including nasopharyngeal carcinoma (NPC). However, the association of this polymorphism with NPC across the published literature has shown conflicting results. We aimed to conduct a case–control study for a possible relation of p53 codon72 Arg>Pro polymorphism with NPC risk in underdeveloped states of India, combine the result with previously available records from different databases and perform a meta-analysis to draw a more definitive conclusion. A total of 70 NPC patients and 70 healthy controls were enrolled from different hospitals of north-eastern India. The p53 codon72 Arg>Pro polymorphism was typed by polymerase chain reaction, which showed an association with NPC risk. In the meta-analysis consisting of 1842 cases and 2330 controls, it was found that individuals carrying the Pro allele and the ProPro genotype were at a significantly higher risk for NPC as compared with those with the Arg allele and the ArgArg genotype, respectively. Individuals with a ProPro genotype and a combined Pro genotype (ProPro+ArgPro) also showed a significantly higher risk for NPC over a wild homozygote ArgArg genotype. Additionally, the strength of each study was tested by power analysis and genotype distribution by Hardy–Weinberg equilibrium. The outcome of the study indicated that both allele frequency and genotype distribution of p53 codon72 Arg>Pro polymorphism were significantly associated with NPC risk. Stratified analyses based on ethnicity and source of samples supported the above result.
Hypotrichosis and juvenile macular dystrophy caused by CDH3 mutation: A candidate disease for retinal gene therapy
Authors: Singh Mandeep S. , Broadgate Suzanne , Mathur Ranjana , Holt Richard , Halford Stephanie , MacLaren Robert E.
Published: May 2016

Hypotrichosis with juvenile macular dystrophy (HJMD) is an autosomal recessive disorder that causes childhood visual impairment. HJMD is caused by mutations in CDH3 which encodes cadherin-3, a protein expressed in retinal pigment epithelium (RPE) cells that may have a key role in intercellular adhesion. We present a case of HJMD and analyse its phenotypic and molecular characteristics to assess the potential for retinal gene therapy as a means of preventing severe visual loss in this condition. Longitudinal in vivo imaging of the retina showed the relative anatomical preservation of the macula, which suggested the presence of a therapeutic window for gene augmentation therapy to preserve visual acuity. The coding sequence of CDH3 fits within the packaging limit of recombinant adeno-associated virus vectors that have been shown to be safe in clinical trials and can efficiently target RPE cells. This report expands the number of reported cases of HJMD and highlights the phenotypic characteristics to consider when selecting candidates for retinal gene therapy.
Correction: Corrigendum: 3D visualization of the lumbar facet joint after degeneration using propagation phase contrast micro-tomography
Authors: Cao Yong , Zhang Yi , Yin Xianzhen , Lu Hongbin , Hu Jianzhong , Duan Chunyue
Published: May 2016

Scientific Reports 6: Article number: 21838; Published online: 24 February 2016; updated: 09 May 2016 The original version of this Article contained a typographical error in the spelling of the author Xianzhen Yin, which was incorrectly given as Xianzheng Yin. This has now been corrected in the PDF and HTML versions of the Article.
Correction: Corrigendum: Sparse deconvolution of high-density super-resolution images
Authors: Hugelier Siewert , de Rooi Johan J. , Bernex Romain , Duwé Sam , Devos Olivier , Sliwa Michel , Dedecker Peter , Eilers Paul H. C. , Ruckebusch Cyril
Published: May 2016

Scientific Reports 6: Article number: 21413; Published online 25 February 2016; Updated: 09 May 2016 A marked-up version of the Supplementary Information was inadvertently published with the original version of this Article. In addition, Supplementary Software 1 was omitted. These errors have now been corrected.
Detection and Quantification of CWD Prions in Fixed Paraffin Embedded Tissues by Real-Time Quaking-Induced Conversion
Authors: Hoover Clare E. , Davenport Kristen A. , Henderson Davin M. , Pulscher Laura A. , Mathiason Candace K. , Zabel Mark D. , Hoover Edward A.
Published: May 2016

Traditional diagnostic detection of chronic wasting disease (CWD) relies on immunodetection of misfolded CWD prion protein (PrPCWD) by western blotting, ELISA, or immunohistochemistry (IHC). These techniques require separate sample collections (frozen and fixed) which may result in discrepancies due to variation in prion tissue distribution and assay sensitivities that limit detection especially in early and subclinical infections. Here, we harness the power of real-time quaking induced conversion (RT-QuIC) to amplify, detect, and quantify prion amyloid seeding activity in fixed paraffin-embedded (FPE) tissue sections. We show that FPE RT-QuIC has greater detection sensitivity than IHC in tissues with low PrPCWD burdens, including those that are IHC-negative. We also employ amyloid formation kinetics to yield a semi-quantitative estimate of prion concentration in a given FPE tissue. We report that FPE RT-QuIC has the ability to enhance diagnostic and investigative detection of disease-associated PrPRES in prion, and potentially other, protein misfolding disease states.
Correction: Corrigendum: Mechanistic analysis of a synthetic inhibitor of the Pseudomonas aeruginosa LasI quorum-sensing signal synthase
Authors: Lidor O. , Al-Quntar A. , Pesci E. C. , Steinberg D.
Published: May 2016

Scientific Reports 5: Article number: 16569; Published online: 23 November 2015; Updated: 09 May 2016 This Article contains typographical errors. In the Results section under subheading ‘In silico evaluation of the interaction between TZD and LasI.’ “A LIGPLOT view of the interaction schema between LasI and TZD-C8 in the three highest energy binding states showed direct hydrogen bonds between the ligand and Arg30 and Ile107 (Supplementary Data Figure S4A)”.
Correction: Corrigendum: Influenza A viruses escape from MxA restriction at the expense of efficient nuclear vRNP import
Authors: Götz Veronika , Magar Linda , Dornfeld Dominik , Giese Sebastian , Pohlmann Anne , Höper Dirk , Kong Byung-Whi , Jans David A. , Beer Martin , Haller Otto , Schwemmle Martin
Published: May 2016

Scientific Reports 6: Article number: 23138; Published online: 18 March 2016; Updated: 09 May 2016 The Acknowledgements section in this Article is incomplete. “We thank Richard Randall for providing A549 cells stably expressing MxA or shMxA, Georg Kochs for providing the NP-specific antibody and Geoffrey Chase, Georg Kochs and Peter Staeheli for critically reading of the manuscript.
Correction: Corrigendum: Multi-stability of circadian phase wave within early postnatal suprachiasmatic nucleus
Authors: Jeong Byeongha , Hong Jin Hee , Kim Hyun , Choe Han Kyoung , Kim Kyungjin , Lee Kyoung J.
Published: May 2016

Scientific Reports 6: Article number: 21463; Published online 19 February 2016; Updated 09 May 2016 The original version of this Article contained errors in the Abstract. “In different SCN cells, oscillations of biochemical markers such as the expression-level of clock genes, are not synchronized but instead form slow circadian phase waves propagating over the whole cell population spatio-temporal struc- ture is a fixed property set by the anatomy of a given SCN.
Galectin-3 Binds to Lubricin and Reinforces the Lubricating Boundary Layer of Articular Cartilage
Authors: Reesink Heidi L. , Bonnevie Edward D. , Liu Sherry , Shurer Carolyn R. , Hollander Michael J. , Bonassar Lawrence J. , Nixon Alan J.
Published: May 2016

Lubricin is a mucinous, synovial fluid glycoprotein that enables near frictionless joint motion via adsorption to the surface of articular cartilage and its lubricating properties in solution. Extensive O-linked glycosylation within lubricin’s mucin-rich domain is critical for its boundary lubricating function; however, it is unknown exactly how glycosylation facilitates cartilage lubrication. Here, we find that the lubricin glycome is enriched with terminal β-galactosides, known binding partners for a family of multivalent lectins called galectins. Of the galectin family members present in synovial fluid, we find that galectin-3 is a specific, high-affinity binding partner for lubricin. Considering the known ability of galectin-3 to crosslink glycoproteins, we hypothesized that galectins could augment lubrication via biomechanical stabilization of the lubricin boundary layer. We find that competitive inhibition of galectin binding results in lubricin loss from the cartilage surface, and addition of multimeric galectin-3 enhances cartilage lubrication. We also find that galectin-3 has low affinity for the surface layer of osteoarthritic cartilage and has reduced affinity for sialylated O-glycans, a glycophenotype associated with inflammatory conditions. Together, our results suggest that galectin-3 reinforces the lubricin boundary layer; which, in turn, enhances cartilage lubrication and may delay the onset and progression of arthritis.
The impact of amplification on differential expression analyses by RNA-seq
Authors: Parekh Swati , Ziegenhain Christoph , Vieth Beate , Enard Wolfgang , Hellmann Ines
Published: May 2016

Currently, quantitative RNA-seq methods are pushed to work with increasingly small starting amounts of RNA that require amplification. However, it is unclear how much noise or bias amplification introduces and how this affects precision and accuracy of RNA quantification. To assess the effects of amplification, reads that originated from the same RNA molecule (PCR-duplicates) need to be identified. Computationally, read duplicates are defined by their mapping position, which does not distinguish PCR- from natural duplicates and hence it is unclear how to treat duplicated reads. Here, we generate and analyse RNA-seq data sets prepared using three different protocols (Smart-Seq, TruSeq and UMI-seq). We find that a large fraction of computationally identified read duplicates are not PCR duplicates and can be explained by sampling and fragmentation bias. Consequently, the computational removal of duplicates does improve neither accuracy nor precision and can actually worsen the power and the False Discovery Rate (FDR) for differential gene expression. Even when duplicates are experimentally identified by unique molecular identifiers (UMIs), power and FDR are only mildly improved. However, the pooling of samples as made possible by the early barcoding of the UMI-protocol leads to an appreciable increase in the power to detect differentially expressed genes.
Joining Chemical Pressure and Epitaxial Strain to Yield Y-doped BiFeO3 Thin Films with High Dielectric Response
Authors: Scarisoreanu N. D. , Craciun F. , Birjega R. , Ion V. , Teodorescu V. S. , Ghica C. , Negrea R. , Dinescu M.
Published: May 2016

BiFeO3 is one of the most promising multiferroic materials but undergoes two major drawbacks: low dielectric susceptibility and high dielectric loss. Here we report high in-plane dielectric permittivity (ε’ ∼2500) and low dielectric loss (tan δ < 0.01) obtained on Bi0.95Y0.05FeO3 films epitaxially grown on SrTiO3 (001) by pulsed laser deposition. High resolution transmission electron microscopy and geometric phase analysis evidenced nanostripe domains with alternating compressive/tensile strain and slight lattice rotations. Nanoscale mixed phase/domain ensembles are commonly found in different complex materials with giant dielectric/electromechanical (ferroelectric/ relaxors) or magnetoresistance (manganites) response. Our work brings insight into the joined role of chemical pressure and epitaxial strain on the appearance of nanoscale stripe structure which creates conditions for easy reorientation and high dielectric response and could be of more general relevance for the field of materials science where engineered materials with huge response to external stimuli are a highly priced target.
Bottom-up synthesis of ordered metal/oxide/metal nanodots on substrates for nanoscale resistive switching memory
Authors: Han Un-Bin , Lee Jang-Sik
Published: May 2016

The bottom-up approach using self-assembled materials/processes is thought to be a promising solution for next-generation device fabrication, but it is often found to be not feasible for use in real device fabrication. Here, we report a feasible and versatile way to fabricate high-density, nanoscale memory devices by direct bottom-up filling of memory elements. An ordered array of metal/oxide/metal (copper/copper oxide/copper) nanodots was synthesized with a uniform size and thickness defined by self-organized nanotemplate mask by sequential electrochemical deposition (ECD) of each layer. The fabricated memory devices showed bipolar resistive switching behaviors confirmed by conductive atomic force microscopy. This study demonstrates that ECD with bottom-up growth has great potential to fabricate high-density nanoelectronic devices beyond the scaling limit of top-down device fabrication processes.
Dynamics of supersonic microparticle impact on elastomers revealed by real–time multi–frame imaging
Authors: Veysset David , Hsieh Alex J. , Kooi Steven , Maznev Alexei A. , Masser Kevin A. , Nelson Keith A.
Published: May 2016

Understanding high–velocity microparticle impact is essential for many fields, from space exploration to medicine and biology. Investigations of microscale impact have hitherto been limited to post–mortem analysis of impacted specimens, which does not provide direct information on the impact dynamics. Here we report real–time multi–frame imaging studies of the impact of 7 μm diameter glass spheres traveling at 700–900 m/s on elastomer polymers. With a poly(urethane urea) (PUU) sample, we observe a hyperelastic impact phenomenon not seen on the macroscale: a microsphere undergoes a full conformal penetration into the specimen followed by a rebound which leaves the specimen unscathed. The results challenge the established interpretation of the behaviour of elastomers under high–velocity impact.
Identification of cancer-driver genes in focal genomic alterations from whole genome sequencing data
Authors: Jang Ho , Hur Youngmi , Lee Hyunju
Published: May 2016

DNA copy number alterations (CNAs) are the main genomic events that occur during the initiation and development of cancer. Distinguishing driver aberrant regions from passenger regions, which might contain candidate target genes for cancer therapies, is an important issue. Several methods for identifying cancer-driver genes from multiple cancer patients have been developed for single nucleotide polymorphism (SNP) arrays. However, for NGS data, methods for the SNP array cannot be directly applied because of different characteristics of NGS such as higher resolutions of data without predefined probes and incorrectly mapped reads to reference genomes. In this study, we developed a wavelet-based method for identification of focal genomic alterations for sequencing data (WIFA-Seq). We applied WIFA-Seq to whole genome sequencing data from glioblastoma multiforme, ovarian serous cystadenocarcinoma and lung adenocarcinoma, and identified focal genomic alterations, which contain candidate cancer-related genes as well as previously known cancer-driver genes.
Immobilization of Polyoxometalate in the Metal-Organic Framework rht-MOF-1: Towards a Highly Effective Heterogeneous Catalyst and Dye Scavenger
Authors: Sun Jing-Wen , Yan Peng-Fei , An Guang-Hui , Sha Jing-Quan , Li Guang-Ming , Yang Guo-Yu
Published: May 2016

A series of three remarkable complexes [PMo12O40]@[Cu6O(TZI)3(H2O)9]4·OH·31H2O (H3TZI = 5-tetrazolylisophthalic acid; denoted as HLJU-1, HLJU = Heilongjiang University), [SiMo12O40]@[Cu6O(TZI)3(H2O)9]4·32H2O (denoted as HLJU-2) and [PW12O40]@[Cu6O(TZI)3(H2O)6]4·OH·31H2O (denoted as HLJU-3) have been isolated by using simple one-step solvothermal reaction of copper chloride, 5-tetrazolylisophthalic acid (H3TZI) and various Keggin-type polyoxometalates (POMs), respectively. Crystal analysis of HLJU 1−3 reveals that Keggin-type polyoxoanions have been fitted snuggly in the cages of rht-MOF-1 (MOF: metal−organic framework) with large cell volume in a range of 87968−88800 Å3 and large pore volume of about 68%. HLJU 1–3 exhibit unique catalytic selectivity and reactivity in the oxidation of alkylbenzene with environmental benign oxidant under mild condition in aqueous phase as well as the uptake capacity towards organic pollutants in aqueous solution.
Plant-derived compounds stimulate the decomposition of organic matter in arctic permafrost soils
Authors: Wild Birgit , Gentsch Norman , Čapek Petr , Diáková Kateřina , Alves Ricardo J. Eloy , Bárta Jiři , Gittel Antje , Hugelius Gustaf , Knoltsch Anna , Kuhry Peter , Lashchinskiy Nikolay , Mikutta Robert , Palmtag Juri , Schleper Christa , Schnecker Jörg , Shibistova Olga , Takriti Mounir , Torsvik Vigdis L. , Urich Tim , Watzka Margarete , Šantrůčková Hana , Guggenberger Georg , Richter Andreas
Published: May 2016

Arctic ecosystems are warming rapidly, which is expected to promote soil organic matter (SOM) decomposition. In addition to the direct warming effect, decomposition can also be indirectly stimulated via increased plant productivity and plant-soil C allocation and this so called “priming effect” might significantly alter the ecosystem C balance. In this study, we provide first mechanistic insights into the susceptibility of SOM decomposition in arctic permafrost soils to priming. By comparing 119 soils from four locations across the Siberian Arctic that cover all horizons of active layer and upper permafrost, we found that an increased availability of plant-derived organic C particularly stimulated decomposition in subsoil horizons where most of the arctic soil carbon is located. Considering the 1,035 Pg of arctic soil carbon, such an additional stimulation of decomposition beyond the direct temperature effect can accelerate net ecosystem C losses and amplify the positive feedback to global warming.
Proteome analysis for the global proteins in the jejunum tissues of enterotoxigenic Escherichia coli -infected piglets
Authors: Ren Wenkai , Yin Jie , Chen Shuai , Duan Jielin , Liu Gang , Li Tiejun , Li Nengzhang , Peng Yuanyi , Tan Bie , Yin Yulong
Published: May 2016

Enterotoxigenic Escherichia coli (ETEC) is a common cause of diarrhea in humans and livestock. In this study, isobaric tags for relative and absolute quantitation (iTRAQ) combined with multidimensional liquid chromatography (LC) and MS analysis was used for screening the differentially expressed proteins in piglet jejunum after ETEC infection. Totally 1,897 proteins were identified with quantitative information in piglet jejunum. We identified 92 differentially expressed proteins in ETEC-induced diarrhea, of which 30 were up regulated and 62 down regulated. Most of the differentially expressed proteins were involved in intestinal function of binding, metabolic process, catalytic activity and immune responses. The inhibition of intestinal immune responses in the jejunum in ETEC-induced diarrhea was also validated by immunobloting and RT-PCR. Our study is the first attempt to analyze the protein profile of ETEC-infected piglets by quantitative proteomics, and our findings could provide valuable information with respect to better understanding the host response to ETEC infection.
Pharmacokinetics and tolerability of NSC23925b, a novel P-glycoprotein inhibitor: preclinical study in mice and rats
Authors: Gao Yan , Shen Jacson K. , Choy Edwin , Zhang Zhan , Mankin Henry J. , Hornicek Francis J. , Duan Zhenfeng
Published: May 2016

Overexpression of P-glycoprotein (Pgp) increases multidrug resistance (MDR) in cancer, which greatly impedes satisfactory clinical treatment and outcomes of cancer patients. Due to unknown pharmacokinetics, the use of Pgp inhibitors to overcome MDR in the clinical setting remains elusive despite promising in vitro results. The purpose of our current preclinical study is to investigate the pharmacokinetics and tolerability of NSC23925b, a novel and potent P-glycoprotein inhibitor, in rodents. Plasma pharmacokinetic studies of single-dose NSC23925b alone or in combination with paclitaxel or doxorubicin were conducted in male BALB/c mice and Sprague-Dawley rats. Additionally, inhibition of human cytochrome P450 (CYP450) by NSC23925b was examined in vitro. Finally, the maximum tolerated dose (MTD) of NSC23925b was determined. NSC23925b displayed favorable pharmacokinetic profiles after intraperitoneal/intravenous (I.P./I.V.) injection alone or combined with chemotherapeutic drugs. The plasma pharmacokinetic characteristics of the chemotherapy drugs were not affected when co-administered with NSC23925b. All the animals tolerated the I.P./I.V. administration of NSC23925b. Moreover, the enzymatic activity of human CYP450 was not inhibited by NSC23925b. Our results demonstrated that Pgp inhibitor NSC23925b exhibits encouraging preclinical pharmacokinetic characteristics and limited toxicity in vivo. NSC23925b has the potential to treat cancer patients with MDR in the future.
Harnessing heterologous and endogenous CRISPR-Cas machineries for efficient markerless genome editing in Clostridium
Authors: Pyne Michael E. , Bruder Mark R. , Moo-Young Murray , Chung Duane A. , Chou C. Perry
Published: May 2016

Application of CRISPR-Cas9 systems has revolutionized genome editing across all domains of life. Here we report implementation of the heterologous Type II CRISPR-Cas9 system in Clostridium pasteurianum for markerless genome editing. Since 74% of species harbor CRISPR-Cas loci in Clostridium, we also explored the prospect of co-opting host-encoded CRISPR-Cas machinery for genome editing. Motivation for this work was bolstered from the observation that plasmids expressing heterologous cas9 result in poor transformation of Clostridium. To address this barrier and establish proof-of-concept, we focus on characterization and exploitation of the C. pasteurianum Type I-B CRISPR-Cas system. In silico spacer analysis and in vivo interference assays revealed three protospacer adjacent motif (PAM) sequences required for site-specific nucleolytic attack. Introduction of a synthetic CRISPR array and cpaAIR gene deletion template yielded an editing efficiency of 100%. In contrast, the heterologous Type II CRISPR-Cas9 system generated only 25% of the total yield of edited cells, suggesting that native machinery provides a superior foundation for genome editing by precluding expression of cas9 in trans. To broaden our approach, we also identified putative PAM sequences in three key species of Clostridium. This is the first report of genome editing through harnessing native CRISPR-Cas machinery in Clostridium.
Screening of an anti-inflammatory peptide from Hydrophis cyanocinctus and analysis of its activities and mechanism in DSS-induced acute colitis
Authors: Zheng Zengjie , Jiang Hailong , Huang Yan , Wang Jie , Qiu Lei , Hu Zhenlin , Ma Xingyuan , Lu Yiming
Published: May 2016

Snake has been used for centuries as a traditional Chinese medicine, especially for therapeutic treatment for inflammatory diseases; however, its mechanisms of action and active constituents remain controversial. In our study, a tumor necrosis factor receptor 1 (TNFR1) selective binding peptide, Hydrostatin-SN1 (H-SN1), which was screened from a Hydrophis cyanocinctus venom gland T7 phage display library, was shown to exhibit significant anti-inflammatory activity in vitro and in vivo. As a TNFR1 antagonist, it reduced cytotoxicity mediated by TNF-α in L929 fibroblasts and effectively inhibited the combination between TNF-α with TNFR1 in surface plasmon resonance analysis. H-SN1 was also shown to suppress TNFR1–associated signaling pathways as it minimized TNF-α-induced NF-кB and MAPK activation in HEK293 embryonic kidney and HT29 adenocarcinoma cell lines. We next determined the effect of H-SN1 in vivo using a murine model of acute colitis induced by dextran sodium sulfate, demonstrating that H-SN1 lowered the clinical parameters of acute colitis including the disease activity index and histologic scores. H-SN1 also inhibited TNF/TNFR1 downstream targets at both mRNA and protein levels. These results indicate that H-SN1 might represent a suitable candidate for use in the treatment of TNF-α-associated inflammatory diseases such as inflammatory bowel diseases.
Semi-automatic recognition of marine debris on beaches
Authors: Ge Zhenpeng , Shi Huahong , Mei Xuefei , Dai Zhijun , Li Daoji
Published: May 2016

An increasing amount of anthropogenic marine debris is pervading the earth’s environmental systems, resulting in an enormous threat to living organisms. Additionally, the large amount of marine debris around the world has been investigated mostly through tedious manual methods. Therefore, we propose the use of a new technique, light detection and ranging (LIDAR), for the semi-automatic recognition of marine debris on a beach because of its substantially more efficient role in comparison with other more laborious methods. Our results revealed that LIDAR should be used for the classification of marine debris into plastic, paper, cloth and metal. Additionally, we reconstructed a 3-dimensional model of different types of debris on a beach with a high validity of debris revivification using LIDAR-based individual separation. These findings demonstrate that the availability of this new technique enables detailed observations to be made of debris on a large beach that was previously not possible. It is strongly suggested that LIDAR could be implemented as an appropriate monitoring tool for marine debris by global researchers and governments.
A novel multi-biofunctional protein from brown rice hydrolysed by endo/endo-exoproteases
Authors: Selamassakul Orrapun , Laohakunjit Natta , Kerdchoechuen Orapin , Ratanakhanokchai Khanok
Published: May 2016

Protein hydrolysate from brown rice is a new source of great multifunctional peptide (biological antioxidant activities, biofunctional properties and bioflavor).
Nonstoichiometric Cu2−xSe nanocrystals in situ produced on the surface of carbon nanotubes for ablation of tumor cells
Authors: Wang Qiang , Li Wen Long , Zou Hong Yan , Liu Hui , Huang Cheng Zhi
Published: May 2016

We fabricate Cu2−xSe/CNT nanohybrids with enhanced photo-thermal performance compared to the individual components and further exploit them for the ablation of cancer cells.
Three-dimensional graphene aerogel–mesoporous carbon composites as novel coatings for solid-phase microextraction for the efficient enrichment of brominated flame retardants
Authors: Wang Xuemei , Lu Muxin , Wang Huan , Huang Pengfei , Ma Xiaomin , Cao Chun , Du Xinzhen
Published: May 2016

Graphene aerogel–mesoporous carbon composites with hierarchical nanostructures were synthesized via a facile, environmentally friendly nanocasting technique for SPME coatings.
Toward rational design of palladium nanoparticles with plasmonically enhanced catalytic performance
Authors: Klinkova Anna , Ahmed Aftab , Choueiri Rachelle M. , Guest Jeffery R. , Kumacheva Eugenia
Published: May 2016

We report plasmonically mediated enhancement of catalytic performance of different Pd-based nanoparticles. Our findings pave the way for design, synthesis and fabrication of Pd nanocatalysts with enhanced performance under visible light illumination.
Far-ultraviolet spectroscopy of solid and liquid states: characteristics, instrumentation, and applications
Authors: Ozaki Yukihiro , Tanabe Ichiro
Published: May 2016

Far-ultraviolet spectroscopy (≥200 nm) can greatly contribute to the basic science of electronic structures for almost all materials and their applications.
Sedimentation coefficient distributions of large particles
Authors: Schuck Peter
Published: May 2016

A uniform mathematical framework for sedimentation coefficient distributions in analytical ultracentrifugation establishes new relationships and resolves differences in analysis methods.
Glycan heterogeneity on gold nanoparticles increases lectin discrimination capacity in label-free multiplexed bioassays
Authors: Otten Lucienne , Vlachou Denise , Richards Sarah-Jane , Gibson Matthew I.
Published: May 2016

The development of new analytical tools as point-of-care biosensors is crucial to combat the spread of infectious diseases, especially in the context of drug-resistant organisms, or to detect biological warfare agents.
Morphology controlled synthesis of platinum nanoparticles performed on the surface of graphene oxide using a gas–liquid interfacial reaction and its application for high-performance electrochemical sensing
Authors: Bai Wushuang , Sheng Qinglin , Zheng Jianbin
Published: May 2016

Electrochemical sensing of nitrite based on morphology-controlled Pt/GO nanocomposites which were obtained using a novel gas–liquid interfacial reaction.
Photoinduced electron transfer in porous organic salt crystals impregnated with fullerenes
Authors: Hasegawa Tetsuya , Ohkubo Kei , Hisaki Ichiro , Miyata Mikiji , Tohnai Norimitsu , Fukuzumi Shunichi
Published: May 2016

Porous organic salt (POS) crystals composed of 9-(4-sulfophenyl)anthracene and triphenylmethylamine were impregnated with fullerenes (C60 and C70), resulting in fluorescence quenching by photoinduced electron transfer.
The stereoselectivity of bipyrrolidine-based sequential polydentate ligands around Ru(ii)
Authors: Popowski Yanay , Goldberg Israel , Kol Moshe
Published: May 2016

The Ru(ii) coordination chemistry of the sequential hexadentate, tetradentate and the novel hybrid pentadentate ligands assembled around the chiral bipyrrolidine core and including bipyridyl and pyridyl periphery units is described.
Non-volatile transistor memory devices using charge storage cross-linked core–shell nanoparticles
Authors: Lo Chen-Tsyr , Watanabe Yu , Oya Hiroshi , Nakabayashi Kazuhiro , Mori Hideharu , Chen Wen-Chang
Published: May 2016

Solution processable cross-linked nanoparticles with a cross-linked conjugated polythiophene core and a hydrophilic shell are firstly explored as charge storage materials for high performance transistor-type memory devices.
Formation of a stable radical by oxidation of a tetraorganoborate
Authors: Braunschweig Holger , Krummenacher Ivo , Mailänder Lisa , Pentecost Leanne , Vargas Alfredo
Published: May 2016

Oxidation of a tetraorganoborate salt leads to selective formation of the corresponding zwitterionic radical rather than carbon–carbon bond formation of the boron substituents.
Control of valence and conduction band energies in layered transition metal phosphates via surface functionalization
Authors: Lentz Levi C. , Kolb Brian , Kolpak Alexie M.
Published: May 2016

Layered transition metal phosphates and phosphites (TMPs) are a class of 2D materials bound together via van der Waals interactions. Through simple functionalization, band energies can be systematically controlled.
A molecular dynamics study of the ionic liquid, choline acetate
Authors: Willcox Jon A. L. , Kim Hyunjin , Kim Hyung J.
Published: May 2016

Choline acetate – a cheap and environmentally friendly ionic liquid – is characterized using molecular dynamics simulations.