bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct observation of spin-layer locking by local Rashba effect in monolayer semiconducting PtSe2 film
Authors: Yao Wei , Wang Eryin , Huang Huaqing , Deng Ke , Yan Mingzhe , Zhang Kenan , Miyamoto Koji , Okuda Taichi , Li Linfei , Wang Yeliang , Gao Hongjun , Liu Chaoxing , Duan Wenhui , Zhou Shuyun 
Published: January 2017

AbstractThe generally accepted view that spin polarization in non-magnetic solids is induced by the asymmetry of the global crystal space group has limited the search for spintronics materials mainly to non-centrosymmetric materials. In recent times it has been suggested that spin polarization originates fundamentally from local atomic site asymmetries and therefore centrosymmetric materials may exhibit previously overlooked spin polarizations. Here, by using spin- and angle-resolved photoemission spectroscopy, we report the observation of helical spin texture in monolayer, centrosymmetric and semiconducting PtSe2 film without the characteristic spin splitting in conventional Rashba effect (R-1). First-principles calculations and effective analytical model analysis suggest local dipole induced Rashba effect (R-2) with spin-layer locking: opposite spins are degenerate in energy, while spatially separated in the top and bottom Se layers. These results not only enrich our understanding of the spin polarization physics but also may find applications in electrically tunable spintronics.
Biomimetically inspired asymmetric total synthesis of (+)-19-dehydroxyl arisandilactone A
Authors: Han Yi-Xin , Jiang Yan-Long , Li Yong , Yu Hai-Xin , Tong Bing-Qi , Niu Zhe , Zhou Shi-Jie , Liu Song , Lan Yu , Chen Jia-Hua , Yang Zhen 
Published: January 2017

AbstractComplex natural products are a proven and rich source of disease-modulating drugs and of efficient tools for the study of chemical biology and drug discovery. The architectures of complex natural products are generally considered to represent significant barriers to efficient chemical synthesis. Here we describe a concise and efficient asymmetric synthesis of 19-dehydroxyl arisandilactone A—which belongs to a family of architecturally unique, highly oxygenated nortriterpenoids isolated from the medicinal plant Schisandra arisanensis. This synthesis takes place by means of a homo-Michael reaction, a tandem retro-Michael/Michael reaction, and Cu-catalysed intramolecular cyclopropanation as key steps. The proposed mechanisms for the homo-Michael and tandem retro-Michael/Michael reactions are supported by density functional theory (DFT) calculation. The developed chemistry may find application for the synthesis of its other family members of Schisandraceae nortriterpenoids.
Elevated-temperature-induced acceleration of PACT clearing process of mouse brain tissue
Authors: Yu Tingting , Qi Yisong , Zhu Jingtan , Xu Jianyi , Gong Hui , Luo Qingming , Zhu Dan 
Published: January 2017

AbstractTissue optical clearing technique shows a great potential for neural imaging with high resolution, especially for connectomics in brain. The passive clarity technique (PACT) is a relative simple clearing method based on incubation, which has a great advantage on tissue transparency, fluorescence preservation and immunostaining compatibility for imaging tissue blocks. However, this method suffers from long processing time. Previous studies indicated that increasing temperature can speed up the clearing. In this work, we aim to systematacially and quantitatively study this influence based on PACT with graded increase of temperatures. We investigated the process of optical clearing of brain tissue block at different temperatures, and found that elevated temperature could accelerate the clearing process and also had influence on the fluorescence intensity. By balancing the advantages with drawbacks, we conclude that 42–47 °C is an alternative temperature range for PACT, which can not only produce faster clearing process, but also retain the original advantages of PACT by preserving endogenous fluorescence well, achieving fine morphology maintenance and immunostaining compatibility.
QuickProbs 2: Towards rapid construction of high-quality alignments of large protein families
Authors: Gudyś Adam , Deorowicz Sebastian 
Published: January 2017

AbstractThe ever-increasing size of sequence databases caused by the development of high throughput sequencing, poses to multiple alignment algorithms one of the greatest challenges yet. As we show, well-established techniques employed for increasing alignment quality, i.e., refinement and consistency, are ineffective when large protein families are investigated. We present QuickProbs 2, an algorithm for multiple sequence alignment. Based on probabilistic models, equipped with novel column-oriented refinement and selective consistency, it offers outstanding accuracy. When analysing hundreds of sequences, Quick-Probs 2 is noticeably better than ClustalΩ and MAFFT, the previous leaders for processing numerous protein families. In the case of smaller sets, for which consistency-based methods are the best performing, QuickProbs 2 is also superior to the competitors. Due to low computational requirements of selective consistency and utilization of massively parallel architectures, presented algorithm has similar execution times to ClustalΩ, and is orders of magnitude faster than full consistency approaches, like MSAProbs or PicXAA. All these make QuickProbs 2 an excellent tool for aligning families ranging from few, to hundreds of proteins.
Joint genome-wide association and transcriptome sequencing reveals a complex polygenic network underlying hypocotyl elongation in rapeseed (Brassica napus L.)
Authors: Luo Xiang , Xue Zhifei , Ma Chaozhi , Hu Kaining , Zeng Ziru , Dou Shengwei , Tu Jinxing , Shen Jinxiong , Yi Bin , Fu Tingdong 
Published: January 2017

AbstractHypocotyl elongation is considered an important typical seedling trait contributing directly to an increase in and stabilization of the yield in Brassica napus, but its molecular genetic mechanism is poorly understood. In the present study, hypocotyl lengths of 210 lines were measured in an illuminated culture room. A genome-wide association study (GWAS) was performed with 23,435 single nucleotide polymorphisms (SNPs) for hypocotyl length. Three lines with long hypocotyl length and three lines with short hypocotyl length from one doubled haploid line (DH) population were used for transcriptome sequencing. A GWAS followed by transcriptome analysis identified 29 differentially expressed genes associated with significant SNPs in B. napus. These genes regulate hypocotyl elongation by mediating flowering morphogenesis, circadian clock, hormone biosynthesis, or important metabolic signaling pathways. Among these genes, BnaC07g46770D negatively regulates hypocotyl elongation directly, as well as flowering time. Our results indicate that a joint GWAS and transcriptome analysis has significant potential for identifying the genes responsible for hypocotyl elongation; The extension of hypocotyl is a complex biological process regulated by a polygenic network.
Identifying the Metabolic Differences of a Fast-Growth Phenotype in Synechococcus UTEX 2973
Authors: Mueller Thomas J. , Ungerer Justin L. , Pakrasi Himadri B. , Maranas Costas D. 
Published: January 2017

AbstractThe photosynthetic capabilities of cyanobacteria make them interesting candidates for industrial bioproduction. One obstacle to large-scale implementation of cyanobacteria is their limited growth rates as compared to industrial mainstays. Synechococcus UTEX 2973, a strain closely related to Synechococcus PCC 7942, was recently identified as having the fastest measured growth rate among cyanobacteria. To facilitate the development of 2973 as a model organism we developed in this study the genome-scale metabolic model iSyu683. Experimental data were used to define CO2 uptake rates as well as the biomass compositions for each strain. The inclusion of constraints based on experimental measurements of CO2 uptake resulted in a ratio of the growth rates of Synechococcus 2973 to Synechococcus 7942 of 2.03, which nearly recapitulates the in vivo growth rate ratio of 2.13. This identified the difference in carbon uptake rate as the main factor contributing to the divergent growth rates. Additionally four SNPs were identified as possible contributors to modified kinetic parameters of metabolic enzymes and candidates for further study. Comparisons against more established cyanobacterial strains identified a number of differences between the strains along with a correlation between the number of cytochrome c oxidase operons and heterotrophic or diazotrophic capabilities.
A new model of sperm nuclear architecture following assessment of the organization of centromeres and telomeres in three-dimensions
Authors: Ioannou Dimitrios , Millan Nicole M. , Jordan Elizabeth , Tempest Helen G. 
Published: January 2017

AbstractThe organization of chromosomes in sperm nuclei has been proposed to possess a unique “hairpin-loop” arrangement, which is hypothesized to aid in the ordered exodus of the paternal genome following fertilization. This study simultaneously assessed the 3D and 2D radial and longitudinal organization of telomeres, centromeres, and investigated whether chromosomes formed the same centromere clusters in sperm cells. Reproducible radial and longitudinal non-random organization was observed for all investigated loci using both 3D and 2D approaches in multiple subjects. We report novel findings, with telomeres and centromeres being localized throughout the nucleus but demonstrating roughly a 1:1 distribution in the nuclear periphery and the intermediate regions with <15% occupying the nuclear interior. Telomeres and centromeres were observed to aggregate in sperm nuclei, forming an average of 20 and 7 clusters, respectively. Reproducible longitudinal organization demonstrated preferential localization of telomeres and centromeres in the mid region of the sperm cell. Preliminary evidence is also provided to support the hypothesis that specific chromosomes preferentially form the same centromere clusters. The more segmental distribution of telomeres and centromeres as described in this study could more readily accommodate and facilitate the sequential exodus of paternal chromosomes following fertilization.
Fast Bayesian inference of optical trap stiffness and particle diffusion
Authors: Bera Sudipta , Paul Shuvojit , Singh Rajesh , Ghosh Dipanjan , Kundu Avijit , Banerjee Ayan , Adhikari R. 
Published: January 2017

AbstractBayesian inference provides a principled way of estimating the parameters of a stochastic process that is observed discretely in time. The overdamped Brownian motion of a particle confined in an optical trap is generally modelled by the Ornstein-Uhlenbeck process and can be observed directly in experiment. Here we present Bayesian methods for inferring the parameters of this process, the trap stiffness and the particle diffusion coefficient, that use exact likelihoods and sufficient statistics to arrive at simple expressions for the maximum a posteriori estimates. This obviates the need for Monte Carlo sampling and yields methods that are both fast and accurate. We apply these to experimental data and demonstrate their advantage over commonly used non-Bayesian fitting methods.
Myosuppressin is involved in the regulation of pupal diapause in the cabbage army moth Mamestra brassicae
Authors: Yamada Nobuto , Kataoka Hiroshi , Mizoguchi Akira 
Published: January 2017

AbstractDiapause, a programmed developmental arrest, is common in insects, enabling them to survive adverse seasons. It is well established that pupal diapause is regulated by ecdysteroids secreted by the prothoracic glands (PGs), with cessation of ecdysteroid secretion after pupal ecdysis leading to pupal diapause. A major factor regulating the gland activity is prothoracicotropic hormone (PTTH) secreted from the brain. In our previous study, we demonstrated that the cessation of PTTH release after pupal ecdysis resulted in the inactivation of the PGs, leading to pupal diapause in the cabbage army moth Mamestra brassicae. Here we show that a neuropeptide myosuppressin also contributes to the inactivation of PGs at the initiation of diapause. Myosuppressin suppresses PTTH-stimulated activation of the PGs in vitro. Concentrations of myosuppressin in the hemolymph after pupal ecdysis are higher in diapause pupae than in nondiapause pupae.
A bias-minimising measure of the influence of head orientation on perceived gaze direction
Authors: Balsdon Tarryn , Clifford Colin W. G. 
Published: January 2017

AbstractThe orientation of the head is an important cue for gaze direction, and its role has been explained in a dual route model. The model incorporates both an attractive and a repulsive effect of head orientation, which act to support accurate gaze perception across large changes in natural stimuli. However, in all previous studies of which we are aware, measurements of the influence of head orientation on perceived gaze direction were obtained using a single-interval methodology, which may have been affected by response bias. Here we compare the single-interval methodology with a two-interval (bias-minimising) design. We find that although measures obtained using the two-interval design showed a stronger attractive effect of head orientation than previous studies, the influence of head orientation on perceived gaze direction still represents a genuine perceptual effect. Measurements obtained using the two-interval design were also shown to be more stable across sessions one week apart. These findings suggest the two-interval design should be used in future experiments, especially if comparing groups who may systematically differ in their biases, such as patients with schizophrenia or autism.
No effect of Bt Cry1Ie toxin on bacterial diversity in the midgut of the Chinese honey bees, Apis cerana cerana (Hymenoptera, Apidae)
Authors: Jia Hui-Ru , Dai Ping-Li , Geng Li-Li , Jack Cameron J. , Li Yun-He , Wu Yan-Yan , Diao Qing-Yun , Ellis James D. 
Published: January 2017

AbstractCry1Ie protein derived from Bacillus thuringiensis (Bt) has been proposed as a promising candidate for the development of a new Bt-maize variety to control maize pests in China. We studied the response of the midgut bacterial community of Apis cerana cerana to Cry1Ie toxin under laboratory conditions. Newly emerged bees were fed one of the following treatments for 15 and 30 days: three concentrations of Cry1Ie toxin (20 ng/mL, 200 ng/mL, and 20 μg/mL) in sugar syrup, pure sugar syrup as a negative control and 48 ng/mL imidacloprid as a positive control. The relative abundance of 16S rRNA genes was measured by Quantitative Polymerase Chain Reaction and no apparent differences were found among treatments for any of these counts at any time point. Furthermore, the midgut bacterial structure and compositions were determined using high-throughput sequencing targeting the V3-V4 regions of the 16S rDNA. All core honey bee intestinal bacterial genera such as Lactobacillus, Bifidobacterium, Snodgrassella, and Gilliamella were detected, and no significant changes were found in the species diversity and richness for any bacterial taxa among treatments at different time points. These results suggest that Cry1Ie toxin may not affect gut bacterial communities of Chinese honey bees.
Accurate discrimination of the wake-sleep states of mice using non-invasive whole-body plethysmography
Authors: Bastianini Stefano , Alvente Sara , Berteotti Chiara , Lo Martire Viviana , Silvani Alessandro , Swoap Steven J. , Valli Alice , Zoccoli Giovanna , Cohen Gary 
Published: January 2017

AbstractA major limitation in the study of sleep breathing disorders in mouse models of pathology is the need to combine whole-body plethysmography (WBP) to measure respiration with electroencephalography/electromyography (EEG/EMG) to discriminate wake-sleep states. However, murine wake-sleep states may be discriminated from breathing and body movements registered by the WBP signal alone. Our goal was to compare the EEG/EMG-based and the WBP-based scoring of wake-sleep states of mice, and provide formal guidelines for the latter. EEG, EMG, blood pressure and WBP signals were simultaneously recorded from 20 mice. Wake-sleep states were scored based either on EEG/EMG or on WBP signals and sleep-dependent respiratory and cardiovascular estimates were calculated. We found that the overall agreement between the 2 methods was 90%, with a high Cohen’s Kappa index (0.82). The inter-rater agreement between 2 experts and between 1 expert and 1 naïve sleep investigators gave similar results. Sleep-dependent respiratory and cardiovascular estimates did not depend on the scoring method. We show that non-invasive discrimination of the wake-sleep states of mice based on visual inspection of the WBP signal is accurate, reliable and reproducible. This work may set the stage for non-invasive high-throughput experiments evaluating sleep and breathing patterns on mouse models of pathophysiology.
Dynamic evolution of hepatitis C virus resistance-associated substitutions in the absence of antiviral treatment
Authors: Eltahla Auda A. , Leung Preston , Pirozyan Mehdi R. , Rodrigo Chaturaka , Grebely Jason , Applegate Tanya , Maher Lisa , Luciani Fabio , Lloyd Andrew R. , Bull Rowena A. 
Published: January 2017

AbstractResistance against new hepatitis C virus (HCV) antivirals is an area of increasing interest. Resistance-associated substitutions (RASs) have been identified in treatment-naïve individuals, but pressures driving treatment-independent RAS emergence are poorly understood. We analysed the longitudinal evolution of RASs in twelve participants with early acute HCV infections. Full-genome deep sequences were analysed for changes in RAS frequency within NS3, NS5A and NS5B-coding regions over the course of the infection. Emergence of RASs relevant only to the polymerase non-nucleoside inhibitors (NNI) was detected, and these lay within CD8+ T-cell epitopes. Conversely, the loss of NNI RASs over time appeared likely to be driven by viral fitness constraints. These results highlight the importance of monitoring CD8+ T cell epitope-associated RASs in populations with dominant HLA types.
Non-AUG start codons responsible for ABO weak blood group alleles on initiation mutant backgrounds
Authors: Cid Emili , Yamamoto Miyako , Yamamoto Fumiichiro 
Published: January 2017

AbstractHisto-blood group ABO gene polymorphism is crucial in transfusion medicine. We studied the activity and subcellular distribution of ABO gene-encoded A glycosyltransferases with N-terminal truncation. We hypothesized that truncated enzymes starting at internal methionines drove the synthesis of oligosaccharide A antigen in those already described alleles that lack a proper translation initiation codon. Not only we tested the functionality of the mutant transferases by expressing them and assessing their capacity to drive the appearance of A antigen on the cell surface, but we also analyzed their subcellullar localization, which has not been described before. The results highlight the importance of the transmembrane domain because proteins deprived of it are not able to localize properly and deliver substantial amounts of antigen on the cell surface. Truncated proteins with their first amino acid well within the luminal domain are not properly localized and lose their enzymatic activity. Most importantly, we demonstrated that other codons than AUG might be used to start the protein synthesis rather than internal methionines in translation-initiation mutants, explaining the molecular mechanism by which transferases lacking a classical start codon are able to synthesize A/B antigens.
Single α-particle irradiation permits real-time visualization of RNF8 accumulation at DNA damaged sites
Authors: Muggiolu Giovanna , Pomorski Michal , Claverie Gérard , Berthet Guillaume , Mer-Calfati Christine , Saada Samuel , Devès Guillaume , Simon Marina , Seznec Hervé , Barberet Philippe 
Published: January 2017

AbstractAs well as being a significant source of environmental radiation exposure, α-particles are increasingly considered for use in targeted radiation therapy. A better understanding of α-particle induced damage at the DNA scale can be achieved by following their tracks in real-time in targeted living cells. Focused α-particle microbeams can facilitate this but, due to their low energy (up to a few MeV) and limited range, α-particles detection, delivery, and follow-up observations of radiation-induced damage remain difficult. In this study, we developed a thin Boron-doped Nano-Crystalline Diamond membrane that allows reliable single α-particles detection and single cell irradiation with negligible beam scattering. The radiation-induced responses of single 3 MeV α-particles delivered with focused microbeam are visualized in situ over thirty minutes after irradiation by the accumulation of the GFP-tagged RNF8 protein at DNA damaged sites.
Mulifunctional Dendritic Emitter: Aggregation-Induced Emission Enhanced, Thermally Activated Delayed Fluorescent Material for Solution-Processed Multilayered Organic Light-Emitting Diodes
Authors: Matsuoka Kenichi , Albrecht Ken , Yamamoto Kimihisa , Fujita Katsuhiko 
Published: January 2017

AbstractThermally activated delayed fluorescence (TADF) materials emerged as promising light sources in third generation organic light-emitting diodes (OLED). Much effort has been invested for the development of small molecular TADF materials and vacuum process-based efficient TADF-OLEDs. In contrast, a limited number of solution processable high-molecular weight TADF materials toward low cost, large area, and scalable manufacturing of solution processed TADF-OLEDs have been reported so far. In this context, we report benzophenone-core carbazole dendrimers (GnB, n = generation) showing TADF and aggregation-induced emission enhancement (AIEE) properties along with alcohol resistance enabling further solution-based lamination of organic materials. The dendritic structure was found to play an important role for both TADF and AIEE activities in the neat films. By using these multifunctional dendritic emitters as non-doped emissive layers, OLED devices with fully solution processed organic multilayers were successfully fabricated and achieved maximum external quantum efficiency of 5.7%.
Polymorphism of apyrimidinic DNA structures in the nucleosome
Authors: Osakabe Akihisa , Arimura Yasuhiro , Matsumoto Syota , Horikoshi Naoki , Sugasawa Kaoru , Kurumizaka Hitoshi 
Published: January 2017

AbstractHuge amounts (>10,000/day) of apurinic/apyrimidinic (AP) sites are produced in genomes, but their structures in chromatin remain undetermined. We determined the crystal structure of the nucleosome containing AP-site analogs at two symmetric sites, which revealed structural polymorphism: one forms an inchworm configuration without an empty space at the AP site, and the other forms a B-form-like structure with an empty space and the orphan base. This unexpected inchworm configuration of the AP site is important to understand the AP DNA repair mechanism, because it may not be recognized by the major AP-binding protein, APE1, during the base excision repair process.