bluuebunny/crossref_metadata_2025_split huggingface dataset:
Solving the woolly mammoth conundrum: amino acid 15N-enrichment suggests a distinct forage or habitat
Authors: Schwartz-Narbonne Rachel , Longstaffe Fred J. , Metcalfe Jessica Z. , Zazula Grant 
Published: June 2015

AbstractUnderstanding woolly mammoth ecology is key to understanding Pleistocene community dynamics and evaluating the roles of human hunting and climate change in late Quaternary megafaunal extinctions. Previous isotopic studies of mammoths’ diet and physiology have been hampered by the ‘mammoth conundrum’: woolly mammoths have anomalously high collagen δ15N values, which are more similar to coeval carnivores than herbivores and which could imply a distinct diet and (or) habitat, or a physiological adaptation. We analyzed individual amino acids from collagen of adult woolly mammoths and coeval species and discovered greater  15N enrichment in source amino acids of woolly mammoths than in most other herbivores or carnivores. Woolly mammoths consumed an isotopically distinct food source, reflective of extreme aridity, dung fertilization and (or) plant selection. This dietary signal suggests that woolly mammoths occupied a distinct habitat or forage niche relative to other Pleistocene herbivores.
Flux of granular particles through a shaken sieve plate
Authors: Wen Pingping , Zheng Ning , Nian Junwei , Li Liangsheng , Shi Qingfan 
Published: June 2015

AbstractWe experimentally investigate a discharging flux of granular particles through a sieve plate subject to vertical vibrations. The mean mass flux shows a non-monotonic relation with the vibration strength. High-speed photography reveals that two stages, the free flight of the particles’ bulk over the plate and the adhesion of the particles’ bulk with the plate, alternately appear, where only the adhesion stage contributes to the flow. With two independent methods, we then measure the adhesion time under different vibration conditions and define an adhesion flux. The adhesion flux monotonically increases with increasing vibration strength. By rescaling the adhesion flux, we find that the adhesion flux is approximately determined by the peak vibration velocity of the shaker. The conclusion is examined with other sieve geometries.
The Effects of Time on Task in Response Selection - An ERP Study of Mental Fatigue
Authors: Möckel Tina , Beste Christian , Wascher Edmund 
Published: June 2015

AbstractLong lasting involvement in a cognitive task leads to mental fatigue. Substantial efforts have been undertaken to understand this phenomenon. However, it has been demonstrated that some changes with time on task are not only related to mental fatigue. The present study intends to clarify these effects of time on task unrelated to mental fatigue on response selection processes at the behavioural and electrophysiological level (using event-related potentials, ERPs). Participants had to perform a Simon task for more than 3 hours and rated their experienced mental fatigue and motivation to continue with the task at several time points during the experiment. The results show that at the beginning of the experiment some unspecific modulations of training and adaptation are evident. With time on task participants’ ability to resolve response conflict appears to become impaired. The results reveal that time on task effects cannot be completely explained by mental fatigue. Instead, it seems that an interplay of adaptation at the beginning and motivational effects in the course of a task modulate performance and neurophysiological parameters. In future studies it will be important to account for the relative contribution of adaptation and motivation parameters when time on task effects are investigated.
Bromide (Br) - Based Synthesis of Ag Nanocubes with High-Yield
Authors: Wu Fan , Wang Wenhui , Xu Zhongfeng , Li Fuli 
Published: June 2015

AbstractThe geometry of metal nanoparticles greatly affects the properties of the localized surface plasmon resonance and surface-enhanced Raman scattering. The synthesis of metal nanoparticles with controllable geometry has thus attracted extensive attentions. In this work, we report a modified polyol synthesis approach of silver (Ag) nanocubes through tuning the concentration of bromide ions (Br− ions). We have systematically investigated the effect of Br− ions in the polyol process and find that higher concentration of Br− ions can enhance oxidative etching effect, which is the dominative factor in determining nanostructure geometry. Therefore, one can realize control over nanostructure geometry by manipulating the concentration of Br− ions. Our work provides an effective approach to control the shape of metallic nanostructures for potential applications.
The radish genome and comprehensive gene expression profile of tuberous root formation and development
Authors: Mitsui Yuki , Shimomura Michihiko , Komatsu Kenji , Namiki Nobukazu , Shibata-Hatta Mari , Imai Misaki , Katayose Yuichi , Mukai Yoshiyuki , Kanamori Hiroyuki , Kurita Kanako , Kagami Tsutomu , Wakatsuki Akihito , Ohyanagi Hajime , Ikawa Hiroshi , Minaka Nobuhiro , Nakagawa Kunihiro , Shiwa Yu , Sasaki Takuji 
Published: June 2015

AbstractUnderstanding the processes that regulate plant sink formation and development at the molecular level will contribute to the areas of crop breeding, food production and plant evolutionary studies. We report the annotation and analysis of the draft genome sequence of the radish Raphanus sativus var. hortensis (long and thick root radish) and transcriptome analysis during root development. Based on the hybrid assembly approach of next-generation sequencing, a total of 383 Mb (N50 scaffold: 138.17 kb) of sequences of the radish genome was constructed containing 54,357 genes. Syntenic and phylogenetic analyses indicated that divergence between Raphanus and Brassica coincide with the time of whole genome triplication (WGT), suggesting that WGT triggered diversification of Brassiceae crop plants. Further transcriptome analysis showed that the gene functions and pathways related to carbohydrate metabolism were prominently activated in thickening roots, particularly in cell proliferating tissues. Notably, the expression levels of sucrose synthase 1 (SUS1) were correlated with root thickening rates. We also identified the genes involved in pungency synthesis and their transcription factors.
Characterization of two-step deglycosylation via oxidation by glycoside oxidoreductase and defining their subfamily
Authors: Kim Eun-Mi , Seo Joo-Hyun , Baek Kiheon , Kim Byung-Gee 
Published: June 2015

AbstractHerein, we report a two-step deglycosylation mediated by the oxidation of glycoside which is different from traditional glycoside hydrolase (GH) mechanism. Previously, we reported a novel flavin adenine dinucleotide (FAD)-dependent glycoside oxidoreductase (FAD-GO) having deglycosylation activity. Various features of the reaction of FAD-GO such as including mechanism and catalytic residue and substrate specificity were studied. In addition, classification of novel FAD-GO subfamily was attempted. Deglycosylation of glycoside was performed spontaneously via oxidation of 3-OH of glycone moiety by FAD-GO mediated oxidation reaction. His493 residue was identified as a catalytic residue for the oxidation step. Interestingly, this enzyme has broad glycone and aglycon specificities. For the classification of FAD-GO enzyme subfamily, putative FAD-GOs were screened based on the FAD-GO from Rhizobium sp. GIN611 (gi 365822256) using BLAST search. The homologs of R. sp. GIN611 included the putative FAD-GOs from Stenotrophomonas strains, Sphingobacterium strains, Agrobacterium tumefaciens str. C58, and etc. All the cloned FAD-GOs from the three strains catalyzed the deglycosylation via enzymatic oxidation. Based on their substrate specificities, deglycosylation and oxidation activities to various ginsenosides, the FAD-GO subfamily members can be utilized as novel biocatalysts for the production of various aglycones.
Highly Efficient Photon Upconversion in Self-Assembled Light-Harvesting Molecular Systems
Authors: Ogawa Taku , Yanai Nobuhiro , Monguzzi Angelo , Kimizuka Nobuo 
Published: June 2015

AbstractTo meet the world’s demands on the development of sunlight-powered renewable energy production, triplet–triplet annihilation-based photon upconversion (TTA–UC) has raised great expectations. However, an ideal highly efficient, low-power and in-air TTA–UC has not been achieved. Here, we report a novel self-assembly approach to achieve this, which enabled highly efficient TTA–UC even in the presence of oxygen. A newly developed lipophilic 9,10-diphenylanthracene-based emitter molecule functionalized with multiple hydrogen-bonding moieties spontaneously coassembled with a triplet sensitizer in organic media, showing efficient triplet sensitization and subsequent triplet energy migration among the preorganized chromophores. This supramolecular light-harvesting system shows a high UC quantum yield of 30% optimized at low excitation power in deaerated conditions. Significantly, the UC emission largely remains even in an air-saturated solution and this approach is facilely applicable to organogel and solid-film systems.
Functional characterization of salicylate hydroxylase from the fungal endophyte Epichloë festucae
Authors: Ambrose Karen V. , Tian Zipeng , Wang Yifei , Smith Jordan , Zylstra Gerben , Huang Bingru , Belanger Faith C. 
Published: June 2015

AbstractEpichloë spp. are symbiotic fungal endophytes of many cool season grasses. The presence of the fungal endophytes often confers insect, drought and disease tolerance to the host grasses. The presence of the fungal endophytes within the host plants does not elicit host defense responses. The molecular basis for this phenomenon is not known. Epichloë festucae, the endophyte of Festuca rubra, expresses a salicylate hydroxylase similar to NahG from the bacterium Pseudomonas putida. Few fungal salicylate hydroxylase enzymes have been reported. The in planta expression of an endophyte salicylate hydroxylase raised the possibility that degradation of plant-produced salicylic acid is a factor in the mechanism of how the endophyte avoids eliciting host plant defenses. Here we report the characterization of the E. festucae salicylate hydroxylase, designated Efe-shyA. Although the fungal enzyme has the expected activity, based on salicylic acid levels in endophyte-free and endophyte-infected plants it is unlikely that expression of the endophyte salicylate hydroxylase is a factor in the lack of a host defense response to the presence of the fungal endophyte.
Short Course Radiation in the Treatment of Localized Rectal cancer: A Systematic Review and Meta-Analysis
Authors: Chen Cui , Sun Peng , Rong Jian , Weng Hui-Wen , Dai Qiang-sheng , Ye Sheng 
Published: June 2015

AbstractThis meta-analysis sets out to systematically assess the efficacy of short course radiation (SRT) for rectal cancer patients based on randomized, controlled trials. Eight randomized controlled trials involving 6894 patients were ultimately included in this meta-analysis. Three trials (n = 2574) compared SRT with surgery alone. Local recurrence was improved (HR = 0.48, 95% CI 0.40 to 0.58). Overall survival was marginally improved with an HR of 0.90 (95% CI 0.81 to 1.00), but the magnitude of benefit was heterogeneous across trials. An additional three trials (n = 3682) compared SRT with selective postoperative radiation ± chemotherapy. A significant reduction of local recurrence (HR = 0.44, 95% CI 0.35 to 0.56) was also found after SRT. However, no benefit in overall survival was observed. Moreover, two trials (n = 638) compared SRT with long course chemoradiation. There was no statistically significant local recurrence or overall survival difference observed between the two strategies. Patients receiving SRT had lower grade 3 or 4 acute treatment related toxicity (RR 0.11, 95% CI 0.05 to 0.22) whereas no difference in late toxicity was observed. Overall, SRT is a reasonable alternative for resectable rectal cancer patients and should be part of an informed discussion of treatment options for this group of patients.
Real Time Tracking of Magmatic Intrusions by means of Ground Deformation Modeling during Volcanic Crises
Authors: Cannavò Flavio , Camacho Antonio G. , González Pablo J. , Mattia Mario , Puglisi Giuseppe , Fernández José 
Published: June 2015

AbstractVolcano observatories provide near real-time information and, ultimately, forecasts about volcano activity. For this reason, multiple physical and chemical parameters are continuously monitored. Here, we present a new method to efficiently estimate the location and evolution of magmatic sources based on a stream of real-time surface deformation data, such as High-Rate GPS and a free-geometry magmatic source model. The tool allows tracking inflation and deflation sources in time, providing estimates of where a volcano might erupt, which is important in understanding an on-going crisis. We show a successful simulated application to the pre-eruptive period of May 2008, at Mount Etna (Italy). The proposed methodology is able to track the fast dynamics of the magma migration by inverting the real-time data within seconds. This general method is suitable for integration in any volcano observatory. The method provides first order unsupervised and realistic estimates of the locations of magmatic sources and of potential eruption sites, information that is especially important for civil protection purposes.
Universal Conductance Fluctuation in Two-Dimensional Topological Insulators
Authors: Choe Duk-Hyun , Chang K. J. 
Published: June 2015

AbstractDespite considerable interest in two-dimensional (2D) topological insulators (TIs), a fundamental question still remains open how mesoscopic conductance fluctuations in 2D TIs are affected by spin-orbit interaction (SOI). Here, we investigate the effect of SOI on the universal conductance fluctuation (UCF) in disordered 2D TIs. Although 2D TI exhibits UCF like any metallic systems, the amplitude of these fluctuations is distinguished from that of conventional spin-orbit coupled 2D materials. Especially, in 2D systems with mirror symmetry, spin-flip scattering is forbidden even in the presence of strong intrinsic SOI, hence increasing the amplitude of the UCF by a factor of "Equation missing" compared with extrinsic SOI that breaks mirror symmetry. We propose an easy way to experimentally observe the existence of such spin-flip scattering in 2D materials. Our findings provide a key to understanding the emergence of a new universal behavior in 2D TIs.
Levodopa in Mucuna pruriens and its degradation
Authors: Pulikkalpura Haridas , Kurup Rajani , Mathew Paravanparampil Jacob , Baby Sabulal 
Published: June 2015

AbstractMucuna pruriens is the best known natural source of L-dopa, the gold standard for treatment of Parkinsonism. M. pruriens varieties are protein rich supplements and are used as food and fodder worldwide. Here, we report L-dopa contents in seeds of fifty six accessions of four M. pruriens varieties, M. pruriens var. pruriens, M. pruriens var. hirsuta, M. pruriens var. utilis and M. pruriens var. thekkadiensis, quantified by HPTLC-densitometry. L-dopa contents varied between 0.58 to 6.42 (%, dr. wt.). High and low L-dopa yielding genotypes/chemotypes of M. pruriens could be multiplied for medicinal and nutritional purposes, respectively. HPTLC profiles of M. pruriens seeds on repeated extraction (24 h) in 1:1 formic acid-alcohol followed by development in butanol:acetic acid:water (4:1:1, v/v) showed consistent degradation of L-dopa (Rf 0.34 ± 0.02) into a second peak (Rf 0.41 ± 0.02). An average of 52.11% degradation of L-dopa was found in seeds of M. pruriens varieties. Since M. pruriens seeds and/or L-dopa are used for treatment of Parkinson’s disease and as an aphrodisiac both in modern and/or traditional systems of medicine, the finding of high level of L-dopa degradation (in pure form and in M. pruriens extracts) into damaging quinones and ROS is very significant.
Tailoring resistive switching in Pt/SrTiO3 junctions by stoichiometry control
Authors: Mikheev Evgeny , Hwang Jinwoo , Kajdos Adam P. , Hauser Adam J. , Stemmer Susanne 
Published: June 2015

AbstractResistive switching effects in transition metal oxide-based devices offer new opportunities for information storage and computing technologies. Although it is known that resistive switching is a defect-driven phenomenon, the precise mechanisms are still poorly understood owing to the difficulty of systematically controlling specific point defects. As a result, obtaining reliable and reproducible devices remains a major challenge for this technology. Here, we demonstrate control of resistive switching based on intentional manipulation of native point defects. Oxide molecular beam epitaxy is used to systematically investigate the effect of Ti/Sr stoichiometry on resistive switching in high-quality Pt/SrTiO3 junctions. We demonstrate resistive switching with improved state retention through the introduction of Ti- and Sr-excess into the near-interface region. More broadly, the results demonstrate the utility of high quality metal/oxide interfaces and explicit control over structural defects to improve control, uniformity and reproducibility of resistive switching processes. Unintentional interfacial contamination layers, which are present if Schottky contacts are processed at low temperature, can easily dominate the resistive switching characteristics and complicate the interpretation if nonstoichiometry is also present.
Ha83, a Chitin Binding Domain Encoding Gene, Is Important to Helicoverpa armigera Nucleopolyhedrovirus Budded Virus Production and Occlusion Body Assembling
Authors: Yu Huan , Xu Jian , Liu Qiang , Liu Tong-Xian , Wang Dun 
Published: June 2015

AbstractHelicoerpa armigera nucleopolyhedrovirus (HearNPV) ha83 is a late expressed gene that encodes a chitin binding protein. Chitin domain truncation studies revealed that the cysteine at the 128 amino acid position probably played an important role in both chitin binding ability and protein transmission of Ha83. In order to study the function of ha83 in the HearNPV infection cycle, an ha83 knockout HearNPV (Ha83KO) was constructed via homologous recombination. Viral growth and viral DNA replication curves showed that fewer budded virions were produced in Ha83KO transfected cells, while viral DNA replication was increased. Electron microscopy revealed that fewer nucleocapsids were transmitted from virogenic stroma in the Ha83KO transfected cell nucleus and the morphology of occlusion bodies was prominently larger and cube-shaped. Furthermore, DNA quantity in occlusion bodies of Ha83KO was significantly lower than the occlusion bodies of HaWT. The transcription analysis indicated that these changes may be due to the decreased expression level of viral structural associated genes, such as polyhedrin, p10, pif-2, or cg30 in Ha83KO infected cells. Above results demonstrated that the cysteine at the 128 amino acid position in Ha83 might be the key amino acid and Ha83 plays an important role in BVs production and OBs assembling.
Electric tuning of magnetization dynamics and electric field-induced negative magnetic permeability in nanoscale composite multiferroics
Authors: Jia Chenglong , Wang Fenglong , Jiang Changjun , Berakdar Jamal , Xue Desheng 
Published: June 2015

AbstractSteering magnetism by electric fields upon interfacing ferromagnetic (FM) and ferroelectric (FE) materials to achieve an emergent multiferroic response bears a great potential for nano-scale devices with novel functionalities. FM/FE heterostructures allow, for instance, the electrical manipulation of magnetic anisotropy via interfacial magnetoelectric (ME) couplings. A charge-mediated ME effect is believed to be generally weak and active in only a few angstroms. Here we present an experimental evidence uncovering a new magnon-driven, strong ME effect acting on the nanometer range. For Co92Zr8(20 nm) film deposited on ferroelectric PMN-PT we show via ferromagnetic resonance (FMR) that this type of linear ME allows for electrical control of simultaneously the magnetization precessionandits damping, both of which are key elements for magnetic switching and spintronics. The experiments unravel further an electric-field-induced negative magnetic permeability effect.
Amino Acid Flux from Metabolic Network Benefits Protein Translation: the Role of Resource Availability
Authors: Hu Xiao-Pan , Yang Yi , Ma Bin-Guang 
Published: June 2015

AbstractProtein translation is a central step in gene expression and affected by many factors such as codon usage bias, mRNA folding energy and tRNA abundance. Despite intensive previous studies, how metabolic amino acid supply correlates with protein translation efficiency remains unknown. In this work, we estimated the amino acid flux from metabolic network for each protein in Escherichia coli and Saccharomyces cerevisiae by using Flux Balance Analysis. Integrated with the mRNA expression level, protein abundance and ribosome profiling data, we provided a detailed description of the role of amino acid supply in protein translation. Our results showed that amino acid supply positively correlates with translation efficiency and ribosome density. Moreover, with the rank-based regression model, we found that metabolic amino acid supply facilitates ribosome utilization. Based on the fact that the ribosome density change of well-amino-acid-supplied genes is smaller than poorly-amino-acid-supply genes under amino acid starvation, we reached the conclusion that amino acid supply may buffer ribosome density change against amino acid starvation and benefit maintaining a relatively stable translation environment. Our work provided new insights into the connection between metabolic amino acid supply and protein translation process by revealing a new regulation strategy that is dependent on resource availability.
HIV Subtypes B and C gp120 and Methamphetamine Interaction: Dopaminergic System Implicates Differential Neuronal Toxicity
Authors: Samikkannu Thangavel , Rao Kurapati V. K. , Salam Abdul Ajees Abdul , Atluri Venkata S. R. , Kaftanovskaya Elena M. , Agudelo Marisela , Perez Suray , Yoo Changwon , Raymond Andrea D. , Ding Hong , Nair Madhavan P. N. 
Published: June 2015

AbstractHIV subtypes or clades differentially induce HIV-associated neurocognitive disorders (HAND) and substance abuse is known to accelerate HIV disease progression. The HIV-1 envelope protein gp120 plays a major role in binding and budding in the central nervous system (CNS) and impacts dopaminergic functions. However, the mechanisms utilized by HIV-1 clades to exert differential effects and the methamphetamine (METH)-associated dopaminergic dysfunction are poorly understood. We hypothesized that clade B and C gp120 structural sequences, modeling based analysis, dopaminergic effect and METH potentiate neuronal toxicity in astrocytes. We evaluated the effect of clade B and C gp120 and/or METH on the DRD-2, DAT, CaMKs and CREBP transcription. Both the structural sequence and modeling studies demonstrated that clade B gp120 in V1-V4, α -2 and N-glycosylated sites are distinct from clade C gp120. The distinct structure and sequence variation of clade B gp120 differentially impact DRD-2, DAT, CaMK II and CaMK IV mRNA, protein and intracellular expression compared to clade C gp120. However, CREB transcription is upregulated by both clade B and C gp120 and METH co-treatment potentiated these effects. In conclusion, distinct structural sequences of HIV-1 clade B and C gp120 differentially regulate the dopaminergic pathway and METH potentiates neurotoxicity.