bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics of skyrmion in disordered chiral magnet of thin film form
Authors: Koshibae Wataru , Nagaosa Naoto 
Published: March 2019

AbstractMagnetic skyrmion is a topological spin texture characterized by the mapping from the two dimensional real space to the unit sphere. It is realized in chiral magnets under an external magnetic field in the plane perpendicular to it. In thin film samples, which are most relevant to the applications, the thickness of the system parallel to the magnetic field is finite, and a skyrmion turns into a skyrmion string, which is often assumed to be a straight rod. There are phenomena related to the internal degrees of freedom along the string, e.g., the monopole and anti-monopole creation/annihilation, corresponding to the change in the skyrmion number. However, the role of this finite thickness in the topological stability and dynamics has not been explored yet. Here we study theoretically the current-driven dynamics of a skyrmion string under disorder potential by systematically changing the thickness of the sample to reveal the dynamical phase diagram in the plane of current density and thickness. We found the three regions, i.e., (i) pinned skyrmion string, (ii) moving depinned skyrmion string, and (iii) annihilation of skyrmion string, for thin and thick limits while (iii) is missing in the intermediate case. This indicates that there is the optimal range of thickness for the topological stability of skyrmion string enhanced compared with a two-dimensional skyrmion. This result provides a way to design and control skyrmions in thin films and interfaces of finite thickness.
An individual participant data meta-analysis on metabolomics profiles for obesity and insulin resistance in European children
Authors: Hellmuth Christian , Kirchberg Franca F. , Brandt Stephanie , Moß Anja , Walter Viola , Rothenbacher Dietrich , Brenner Hermann , Grote Veit , Gruszfeld Dariusz , Socha Piotr , Closa-Monasterolo Ricardo , Escribano Joaquin , Luque Veronica , Verduci Elvira , Mariani Benedetta , Langhendries Jean-Paul , Poncelet Pascale , Heinrich Joachim , Lehmann Irina , Standl Marie , Uhl Olaf , Koletzko Berthold , Thiering Elisabeth , Wabitsch Martin 
Published: March 2019

AbstractChildhood obesity prevalence is rising in countries worldwide. A variety of etiologic factors contribute to childhood obesity but little is known about underlying biochemical mechanisms. We performed an individual participant meta-analysis including 1,020 pre-pubertal children from three European studies and investigated the associations of 285 metabolites measured by LC/MS-MS with BMI z-score, height, weight, HOMA, and lipoprotein concentrations. Seventeen metabolites were significantly associated with BMI z-score. Sphingomyelin (SM) 32:2 showed the strongest association with BMI z-score (P = 4.68 × 10−23) and was also closely related to weight, and less strongly to height and LDL, but not to HOMA. Mass spectrometric analyses identified SM 32:2 as myristic acid containing SM d18:2/14:0. Thirty-five metabolites were significantly associated to HOMA index. Alanine showed the strongest positive association with HOMA (P = 9.77 × 10−16), while acylcarnitines and non-esterified fatty acids were negatively associated with HOMA. SM d18:2/14:0 is a powerful marker for molecular changes in childhood obesity. Tracing back the origin of SM 32:2 to dietary source in combination with genetic predisposition will path the way for early intervention programs. Metabolic profiling might facilitate risk prediction and personalized interventions in overweight children.
Efficient Genomic Interval Queries Using Augmented Range Trees
Authors: Mao Chengsheng , Eran Alal , Luo Yuan 
Published: March 2019

AbstractEfficient large-scale annotation of genomic intervals is essential for personal genome interpretation in the realm of precision medicine. There are 13 possible relations between two intervals according to Allen’s interval algebra. Conventional interval trees are routinely used to identify the genomic intervals satisfying a coarse relation with a query interval, but cannot support efficient query for more refined relations such as all Allen’s relations. We design and implement a novel approach to address this unmet need. Through rewriting Allen’s interval relations, we transform an interval query to a range query, then adapt and utilize the range trees for querying. We implement two types of range trees: a basic 2-dimensional range tree (2D-RT) and an augmented range tree with fractional cascading (RTFC) and compare them with the conventional interval tree (IT). Theoretical analysis shows that RTFC can achieve the best time complexity for interval queries regarding all Allen’s relations among the three trees. We also perform comparative experiments on the efficiency of RTFC, 2D-RT and IT in querying noncoding element annotations in a large collection of personal genomes. Our experimental results show that 2D-RT is more efficient than IT for interval queries regarding most of Allen’s relations, RTFC is even more efficient than 2D-RT. The results demonstrate that RTFC is an efficient data structure for querying large-scale datasets regarding Allen’s relations between genomic intervals, such as those required by interpreting genome-wide variation in large populations.
Investigation of multiple-dynein transport of melanosomes by non-invasive force measurement using fluctuation unit χ
Authors: Hasegawa Shin , Sagawa Takashi , Ikeda Kazuho , Okada Yasushi , Hayashi Kumiko 
Published: March 2019

AbstractPigment organelles known as melanosomes disperse or aggregate in a melanophore in response to hormones. These movements are mediated by the microtubule motors kinesin-2 and cytoplasmic dynein. However, the force generation mechanism of dynein, unlike that of kinesin, is not well understood. In this study, to address this issue, we investigated the dynein-mediated aggregation of melanosomes in zebrafish melanophores. We applied the fluctuation theorem of non-equilibrium statistical mechanics to estimate forces acting on melanosomes during transport by dynein, given that the energy of a system is related to its fluctuation. Our results demonstrate that multiple force-producing units cooperatively transport a single melanosome. Since the force is generated by dynein, this suggests that multiple dyneins carry a single melanosome. Cooperative transport has been reported for other organelles; thus, multiple-motor transport may be a universal mechanism for moving organelles within the cell.
Prediction of soil salinity with soil-reflected spectra: A comparison of two regression methods
Authors: Zhang Xiaoguang , Huang Biao 
Published: March 2019

AbstractTo achieve the best high spectral quantitative inversion of salt-affected soils, typical saline-sodic soil was selected from northeast China, and the soil spectra were measured; then, partial least-squares regression (PLSR) models and principle component regression(PCR) models were established for soil spectral reflectance and soil salinity, respectively. Modelling accuracies were compared between two models and conducted with different spectrum processing methods and different sampling intervals. Models based on all of the original spectral bands showed that the PLSR was superior to the PCR; however, after smoothing the spectra data, the PLSR did not continue outperforming the PCR. Models established by various transformed spectra after smoothing did not continue showing superiority of the PCR over the PLSR; therefore, we can conclude that the prediction accuracies of the models were not only determined by the smoothing methods, but also by spectral mathematical transformations. The best model was the PCR based on the median filtering data smoothing technique (MF) + log (1/X) + baseline correction transformation (R2 = 0.7206 and RMSE = 0.3929). To keep the information loss becoming too large, this suggested that an 8 nm sampling interval was the best when using soil spectra to predict soil salinity for both the PLSR and PCR models.
Lithium ion trapping mechanism of SiO2 in LiCoO2 based memristors
Authors: Hu Qi , Li Runmiao , Zhang Xinjiang , Gao Qin , Wang Mei , Shi Hongliang , Xiao Zhisong , Chu Paul K. , Huang Anping 
Published: March 2019

AbstractPt/LiCoO2/SiO2/Si stacks with different SiO2 thicknesses are fabricated and the influence of SiO2 on memristive behavior is investigated. It is demonstrated that SiO2 can serve as Li ion trapping layer benefiting device retention, and the thickness of SiO2 must be controlled to avoid large SET voltage and state instability. Simulation model based on Nernst potential and diffusion potential is postulated for electromotive force in LiCoO2 based memristors. The simulation results show that SiO2 trapping layer decreases the total electromotive field of device and thereby prevents Li ions from migrating back to LiCoO2. This model shows a good agreement with experimental data and reveals the Li ion trapping mechanism of SiO2 in LiCoO2 based memristors.
Gene Duplication Associated with Increased Fluconazole Tolerance in Candida auris cells of Advanced Generational Age
Authors: Bhattacharya Somanon , Holowka Thomas , Orner Erika P. , Fries Bettina C. 
Published: March 2019

AbstractCandida auris is an emerging multi-drug resistant yeast that causes systemic infections. Here we show that C. auris undergoes replicative aging (RA) that results from asymmetric cell division and causes phenotypic differences between mother and daughter cells similar to other pathogenic yeasts. Importantly, older C. auris cells (10 generations) exhibited higher tolerance to fluconazole (FLC), micafungin, 5- flucytosine and amphotericin B compared to younger (0–3 generation) cells. Increased FLC tolerance was associated with increased Rhodamine 6G (R6G) efflux and therapeutic failure of FLC in a Galleria infection model. The higher efflux in the older cells correlated with overexpression of the efflux pump encoding gene CDR1 (4-fold). In addition, 8-fold upregulation of the azole target encoding gene ERG11 was noted in the older cells. Analysis of genomic DNA from older cells by qPCR indicates that transient gene duplication of CDR1 and ERG11 causes the observed age-dependent enhanced FLC tolerance in C. auris strains. Furthermore, older cells exhibited a thickened cell wall, decreased neutrophil killing (24% vs 50%), increased epithelial cell adhesion (31.6% vs 17.8%) and upregulation of adhesin protein Als5p. Thus, this study demonstrates that transient gene duplication can occur during RA, causing increased FLC tolerance in old C. auris cells.
Generation of a Fully Human scFv that binds Tumor-Specific Glycoforms
Authors: Lu Zhongpeng , Kamat Kalika , Johnson Blake P. , Yin Catherin C. , Scholler Nathalie , Abbott Karen L. 
Published: March 2019

AbstractTumor-specific glycosylation changes are an attractive target for the development of diagnostic and therapeutic applications. Periostin is a glycoprotein with high expression in many tumors of epithelial origin including ovarian cancer. Strategies to target the peptide portion of periostin as a diagnostic or therapeutic biomarker for cancer are limited due to increased expression of periostin in non-cancerous inflammatory conditions. Here, we have screened for antibody fragments that recognize the tumor-specific glycosylation present on glycoforms of periostin containing bisecting N-glycans in ovarian cancer using a yeast-display library of antibody fragments, while subtracting those that bind to the periostin protein with glycoforms found in non-malignant cell types. We generated a biotinylated form of a fully human scFv antibody (scFvC9) that targets the bisecting N-glycans expressed by cancer cells. Validation studies in vitro and in vivo using scFvC9 indicate this antibody can be useful for the development of diagnostic, imaging, and therapeutic applications for cancers that express the antigen.
Coherent power amplification of third-order harmonic femtosecond pulses at thin-film up-conversion nanoparticles
Authors: Gao Yi , Lee Hyub , Xu Wen , Jiao Jiannan , Chen Peng , Kim Dong-Hwan , Kim Young-Jin 
Published: March 2019

AbstractThird harmonic generation (THG) is a nonlinear optical process attractive in high-resolution interfacial studies, sub-wavelength light manipulation, and bio-molecular detection due to its capability of converting low-energy quanta into a quantum of a higher energy. One of the limitations in utilizing THG is its low power conversion efficiency; thus, various THG enhancement methods have been researched by involving plasmonic coupling effects or utilizing electric band gap resonances at quantum dots or two-dimensional materials. Meanwhile, lanthanide ion-doped up-conversion nanoparticles (UCNPs) can be excited by a multi-photon process similar to THG, but its interaction or resonance with THG has not been studied to date. In this Communication, we demonstrate the first coherent amplification of third-order harmonic femtosecond pulses at multi-layered UCNP thin-film with an amplification factor of 7.8. This amplification is made by the resonance interaction of incident femtosecond laser field, generated third-order harmonics, and the electric band gaps of UCNPs. The power contribution of the third-order harmonic and the up-conversion luminescence (UCL) is strongly dependent on the sample geometry due to the reabsorption effect. For in-depth understanding of the emission characteristics, spectral-domain, time-domain, radio-frequency (RF) domain, and polarization-dependence analysis were addressed. This coherent amplification of third harmonic (TH) at UCNP thin-films enables us to attain higher power, shorter wavelength, and ultra-short femtosecond pulses generated from a simple thin-film structure near to the target samples, which will pave a way to an ultrafast short-wavelength laser platform for material characterization, sub-wavelength photonics, and biomolecular detection.
D-Serine reflects kidney function and diseases
Authors: Hesaka Atsushi , Sakai Shinsuke , Hamase Kenji , Ikeda Tatsuhiko , Matsui Rakan , Mita Masashi , Horio Masaru , Isaka Yoshitaka , Kimura Tomonori 
Published: March 2019

AbstractD-Amino acids, long-term undetected enantiomers of L-amino acids, are now emerging as potential biomarkers, especially for kidney diseases. Management of chronic kidney disease (CKD), a global problem with its high prevalence and poor prognosis, is currently unsatisfactory due to the difficulty in estimating kidney function and in early detection of diseases. We now show that intra-body dynamics of D-serine reflect kidney function and diseases. The blood level of D-serine correlated well with the actual glomerular filtration ratio, a key kidney function. This correlation was compatible with those of conventional kidney markers, and blood level of D-serine was relatively unaffected by such clinical factors as body size. The balance between excretion and reabsorption of amino acids by the kidney was controlled with chiral selectivity, and the reabsorption of D-serine was sensitive to the presence of CKD. The combination of blood level and urinary dynamics of D-serine effectively distinguished CKD from non-CKD. These lines of evidence provide new insights into the enantioselective amino acid dynamics in the human body that reflect disease pathophysiology. D-Serine may serve as a vital biomarker that suppress CKD onset through the precise assessment of kidney function and the diagnosis of CKD.
Demonstration of extrinsic chirality of photoluminescence with semiconductor-metal hybrid nanowires
Authors: Hakkarainen Teemu , Petronijevic Emilija , Rizzo Piton Marcelo , Sibilia Concita 
Published: March 2019

AbstractChiral optical response is an inherent property of molecules and nanostructures, which cannot be superimposed on their mirror images. In specific cases, optical chirality can be observed also for symmetric structures. This so-called extrinsic chirality requires that the mirror symmetry is broken by the geometry of the structure together with the incident or emission angle of light. From the fabrication point of view, the benefit of extrinsic chirality is that there is no need to induce structural chirality at nanoscale. This paper reports demonstration extrinsic chirality of photoluminescence emission from asymmetrically Au-coated GaAs-AlGaAs-GaAs core-shell nanowires fabricated on silicon by a completely lithography-free self-assembled method. In particular, the extrinsic chirality of PL emission is shown to originate from a strong symmetry breaking of fundamental HE11 waveguide modes due to the presence of the asymmetric Au coating, causing preferential emission of left and right-handed emissions in different directions in the far field.
Sensitivity of speleothem records in the Indian Summer Monsoon region to dry season infiltration
Authors: Ronay Elli R. , Breitenbach Sebastian F. M. , Oster Jessica L. 
Published: March 2019

AbstractIn climates with strongly seasonal rainfall, speleothem-based paleoclimate reconstructions are often thought to reflect wet season conditions, assuming a bias toward the season with greater water supply. This is particularly true in monsoon regions, where speleothem records are interpreted to document monsoon strength changes on multiple timescales. Dry season infiltration variability and rainfall seasonality are not typically considered in these reconstructions, even though cave ventilation could bias speleothem growth toward the cooler season. To investigate the influence of dry season infiltration on speleothem geochemistry, we combine a modern, sub-seasonally resolved trace element record from Mawmluh Cave in Northeast India with forward modeling experiments. We find that variations in the amplitude of seasonal signals in speleothem Mg/Ca, which reflects prior carbonate precipitation, are more sensitive to dry season rather than monsoon season infiltration. This sensitivity may be enhanced by dry season cave ventilation. The Mawmluh speleothem Mg/Ca record is consistent with increased dry season rainfall during the 1976–1998 warm phase of the Pacific Decadal Oscillation relative to 1964–2013. Our work demonstrates the importance of considering non-monsoon season rainfall when interpreting speleothem paleoclimate records and suggests that trace elements could provide insight into periods of enhanced dry season infiltration in monsoonal climates.
Hox gene expression determines cell fate of adult periosteal stem/progenitor cells
Authors: Bradaschia-Correa Vivian , Leclerc Kevin , Josephson Anne M. , Lee Sooyeon , Palma Laura , Litwa Hannah P. , Neibart Shane S. , Huo Jason C. , Leucht Philipp 
Published: March 2019

AbstractHox genes are evolutionarily conserved transcription factors that during embryonic development function as master regulators of positional identity. In postnatal life, the function of Hox proteins is less clear: Hox genes are expressed during tissue repair, but in this context their function(s) are largely unknown. Here we show that Hox genes are expressed in periosteal stem/progenitor cells in a distribution similar to that during embryonic development. Using unbiased sequencing, we established that periosteal stem/progenitor cells from distinct anatomic sites within the skeleton significantly differ in their transcriptome, and that Hox expression status best defines these differences. Lastly, we provide evidence that Hox gene expression is one potential mechanism that maintains periosteal stem/progenitor cells in a more primitive, tripotent state, while suppression of Hox genes leads to fate changes with loss of tripotency. Together, our data describe an adult role of Hox genes other than positional identity, and the modulatory role of Hox genes in fate decisions may offer potential druggable targets for the treatment of fractures, non-unions and bone defects.
A multidirectional beam steering reflector actuated by hydraulic control
Authors: Liu Chao , Wang Di , Wang Qiong-Hua 
Published: March 2019

AbstractThis paper presents a multidirectional beam steering reflector (MBSR) actuated by hydraulic control. It consists of three substrates, an elastic membrane, a magnetic base and a mirror reflector (MR). The MR is fixed on the magnetic base and covered upon the top substrate. The bottom substrate is designed with three channels for pulling in/out the liquid. When liquid volume changes, the shape of the elastic membrane changes to form a liquid piston, accordingly. The liquid piston can make the MR rotate to different directions. When a light beam irradiates the MR, it can achieve the function of beam steering in latitude and longitude, simultaneously. Our experiments show that the proposed MBSR can deflect the light beam through a maximum angle of 0~12.7° in latitude and six-directions in longitude. The MBSR has potential applications in the fields of free-space optical communications, laser detections and solar cells.
Alternative reproductive adaptations predict asymmetric responses to climate change in lizards
Authors: Jara Manuel , García-Roa Roberto , Escobar Luis E. , Torres-Carvajal Omar , Pincheira-Donoso Daniel 
Published: March 2019

AbstractAnthropogenic climate change ranks among the major global-scale threats to modern biodiversity. Extinction risks are known to increase via the interactions between rapid climatic alterations and environmentally-sensitive species traits that fail to adapt to those changes. Accumulating evidence reveals the influence of ecophysiological, ecological and phenological factors as drivers underlying demographic collapses that lead to population extinctions. However, the extent to which life-history traits influence population responses to climate change remains largely unexplored. The emerging ‘cul-de-sac hypothesis’ predicts that reptilian viviparity (‘live-bearing’ reproduction), a ‘key innovation’ facilitating historical invasions of cold climates, increases extinction risks under progressively warming climates compared to oviparous reproduction – as warming advances polewards/mountainwards, historically cold-climates shrink, leading viviparous species to face demographic collapses. We present the first large-scale test of this prediction based on multiple lizard radiations and on future projections of climate-based ecological niche models. Viviparous species were found to experience stronger elevational range shifts (and potentially increased extinctions) in coming decades, compared to oviparous lizards. Therefore, our analyses support the hypothesis’s fundamental prediction that elevational shifts are more severe in viviparous species, and highlight the role that life-history adaptations play in the responses of biodiversity to ongoing climate change.
Biochar phosphorus concentration dictates mycorrhizal colonisation, plant growth and soil phosphorus cycling
Authors: Solaiman Zakaria M. , Abbott Lynette K. , Murphy Daniel V. 
Published: March 2019

AbstractWe aimed to determine the relationship between biochar properties and colonisation of roots by arbuscular mycorrhizal (AM) fungi in agricultural soil. We used a range of biochars that differed in pH, water holding capacity, C, N and P concentrations to investigate interactions between biochar and AM fungi. A glasshouse experiment was conducted with subterranean clover and wheat, amended separately with 34 sources of biochar (applied at 1% w/w), to investigate potential responses in a phosphorus (P) deficient agricultural soil. Plant growth responses to biochar ranged from positive to negative and were dependent on biochar P concentration, available soil P and AM root colonisation. The higher the nutrient P concentration in biochar, the lower was AM colonisation. Growth responses of wheat and clover to the application of various biochars were mostly positive, and their growth was correlated, but biochar contributions to soil fertility varied with biochar properties. When nutrient concentrations are higher in biochars, especially for P and N, plants can gain access to nutrients via the plant roots and mycorrhizal hyphae. Thus biochar amendments can increase both plant nutrient uptake and crop production in nutrient deficient soil.