bluuebunny/crossref_metadata_2025_split huggingface dataset:
Demonstrative operation of four-terminal memristive devices fabricated on reduced TiO2 single crystals
Authors: Takeuchi Shotaro , Shimizu Takuma , Isaka Tsuyoshi , Tohei Tetsuya , Ikarashi Nobuyuki , Sakai Akira 
Published: February 2019

AbstractResistive switching (RS) was demonstrated in four-terminal planar memristive devices fabricated on reduced TiO2 (TiO2−x) single crystal substrates. In the device, a pair of diagonally opposing electrode terminals is used to modify the distribution of oxygen vacancies in the region between another pair of diagonally opposing electrode terminals. This allowed microscopic visual observations of the oxygen vacancy distribution based on electrocoloring. The visual contrast observed in the TiO2−x reflects the oxygen vacancy concentration in the electrically active zone of the device, which can be modified by application of various external voltages to the electrodes. The current that flows in the device is significantly dependent on the modified oxygen vacancy distribution and the resultant resistance is switchable when the polarization of the applied external voltage is reversed. The crystallographic orientation of the TiO2−x substrate has a strong influence on the reversible RS phenomenon. Mechanisms behind the voltage-driven resistance change are elaborated with the aid of microscopic analysis for both crystalline and electronic structures in the electrically active zone of the device. Suppression of the formation of irreversible conductive structures comprised of accumulated oxygen vacancies is a key to establishing reversible RS in the device.
Characterization of the mitochondrial genome of an ancient amphipod Halice sp. MT-2017 (Pardaliscidae) from 10,908 m in the Mariana Trench
Authors: Li Jun-yuan , Zeng Cong , Yan Guo-yong , He Li-sheng 
Published: February 2019

AbstractSmall amphipods (Halice sp. MT-2017) with body length <1 cm were collected from the Challenger Deep (~10,920 m below sea level). The divergence time of their lineage was approximately 109 Mya, making this group ancient compared to others under study. The mitochondrial genome of Halice sp. shared the usual gene components of metazoans, comprising 13 protein coding genes (PCGs), 22 transfer RNAs (tRNAs), and 2 ribosomal RNAs (rRNAs). The arrangement of these genes, however, differed greatly from that of other amphipods. Of the 15 genes that were rearranged with respect to the pancrustacean gene pattern, 12 genes (2 PCGs, 2 rRNAs, and 8 tRNAs) were both translocated and strand-reversed. In contrast, the mitochondrial genomes in other amphipods never show so many reordered genes, and in most instances, only tRNAs were involved in strand-reversion-coupled translocation. Other characteristics, including reversed strand nucleotide composition bias, relatively higher composition of non-polar amino acids, and lower evolutionary rate, were also identified. Interestingly, the latter two features were shared with another hadal amphipod, Hirondellea gigas, suggesting their possible associations with the adaptation to deep-sea extreme habitats. Overall, our data provided a useful resource for future studies on the evolutionary and adaptive mechanisms of hadal faunas.
Optical bleaching front in bedrock revealed by spatially-resolved infrared photoluminescence
Authors: Sellwood E. L. , Guralnik B. , Kook M. , Prasad A. K. , Sohbati R. , Hippe K. , Wallinga J. , Jain M. 
Published: February 2019

AbstractOptically stimulated luminescence (OSL) dating of sediment, based on the accumulation of trapped charge in natural crystals since their last exposure to daylight, has revolutionised our understanding of the late Quaternary period. Recently, a complementary technique called luminescence rock surface dating (RSD), which uses differential spatial eviction of trapped charges in rocks exposed to daylight, has been developed to derive exposure and burial ages, and hard-rock erosion rates. In its current form, the RSD technique suffers from labour intensive sample preparation, uncertainties in the depth and dose rate estimates, and poor resolution of the luminescence-depth profile. Here, we develop a novel, 2D luminescence imaging technique for RSD of large rock slabs (3 × 5 cm) to overcome these challenges. We utilize the recently discovered infrared photoluminescence (IRPL) signal for direct, non-destructive imaging of the luminescence-depth profile in a sub-aerially exposed granitic rock, with an unprecedented spatial resolution of ~140 µm. We further establish a correlation between luminescence and geochemistry using micro X-ray fluorescence (µXRF) spectroscopy. Our study promises a substantial advancement in luminescence imaging and paves the path towards novel applications using 2D dating, micro-dosimetry in mixed composition samples, and portable instrumentation for in-situ luminescence measurements.
KRAS genotyping by digital PCR combined with melting curve analysis
Authors: Tanaka Junko , Nakagawa Tatsuo , Shiratori Akiko , Shimazaki Yuzuru , Uematsu Chihiro , Kamahori Masao , Yokoi Takahide , Harada Kunio , Kohara Yoshinobu 
Published: February 2019

AbstractDigital PCR (dPCR) has been developed as a method that can quantify nucleic acids more sensitively than real-time PCR. However, dPCR exhibits large fluctuations in the fluorescence intensity of the compartment, resulting in low accuracy. The main cause is most likely due to insufficient PCR. In this study, we proposed a new method that combines dPCR with melting curve analysis and applied that method to KRAS genotyping. Since the melting temperature (Tm) of the PCR product hardly depends on the amplification efficiency, genotyping accuracy is improved by using the Tm value. The results showed that the peaks of the distribution of the Tm values of DNA in the wells were 68.7, 66.3, and 62.6 °C for wild-type KRAS, the G12R mutant, and the G12D mutant, respectively, and the standard deviation of the Tm values was 0.2 °C for each genotype. This result indicates that the proposed method is capable of discriminating between the wild-type sequence and the two mutants. To the best of our knowledge, this is the first demonstration of the genotyping of single mutations by combining melting curve analysis and dPCR. The application of this approach could be useful for the quantification and genotyping of cancer-related genes in low-abundance samples.
Pareto Optimality Explanation of the Glycolytic Alternatives in Nature
Authors: Ng Chiam Yu , Wang Lin , Chowdhury Anupam , Maranas Costas D. 
Published: February 2019

AbstractThe Entner-Doudoroff (ED) and Embden-Meyerhof-Parnas (EMP) glycolytic pathways are largely conserved across glycolytic species in nature. Is this a coincidence, convergent evolution or there exists a driving force towards either of the two pathway designs? We addressed this question by first employing a variant of the optStoic algorithm to exhaustively identify over 11,916 possible routes between glucose and pyruvate at different pre-determined stoichiometric yields of ATP. Subsequently, we analyzed the thermodynamic feasibility of all the pathways at physiological metabolite concentrations and quantified the protein cost of the feasible solutions. Pareto optimality analysis between energy efficiency and protein cost reveals that the naturally evolved ED and EMP pathways are indeed among the most protein cost-efficient pathways in their respective ATP yield categories and remain thermodynamically feasible across a wide range of ATP/ADP ratios and pathway intermediate metabolite concentration ranges. In contrast, pathways with higher ATP yield (>2) while feasible, are bound within stringent and often extreme operability ranges of cofactor and intermediate metabolite concentrations. The preponderance of EMP and ED is thus consistent with not only optimally balancing energy yield vs. enzyme cost but also with ensuring operability for wide metabolite concentration ranges and ATP/ADP ratios.
Impulsivity and body fat accumulation are linked to cortical and subcortical brain volumes among adolescents and adults
Authors: Kakoschke Naomi , Lorenzetti Valentina , Caeyenberghs Karen , Verdejo-García Antonio 
Published: February 2019

AbstractObesity is associated not only with metabolic and physical health conditions, but with individual variations in cognition and brain health. This study examined the association between body fat (an index of excess weight severity), impulsivity (a vulnerability factor for obesity), and brain structure among adolescents and adults across the body mass index (BMI) spectrum. We used 3D T1 weighted anatomic magnetic resonance imaging scans to map the association between body fat and volumes in regions associated with obesity and impulsivity. Participants were 127 individuals (BMI: 18–40 kg/m2;M = 25.69 ± 5.15), aged 14 to 45 years (M = 24.79 ± 9.60; female = 64). Body fat was measured with bioelectric impendence technology, while impulsivity was measured with the UPPS-P Impulsive Behaviour Scale. Results showed that higher body fat was associated with larger cerebellar white matter, medial orbitofrontal cortex (OFC), and nucleus accumbens volume, although the latter finding was specific to adolescents. The relationship between body fat and medial OFC volume was moderated by impulsivity. Elevated impulsivity was also associated with smaller amygdala and larger frontal pole volumes. Our findings link vulnerability and severity markers of obesity with neuroanatomical measures of frontal, limbic and cerebellar structures, and unravel specific links between body fat and striatal volume in adolescence.
Circular RNAs are temporospatially regulated throughout development and ageing in the rat
Authors: Mahmoudi E. , Cairns M. J. 
Published: February 2019

AbstractCircular RNAs (circRNAs) are covalently closed structural isoforms of linear mRNA which have been observed across a broad range of species and tissues. Here, we provide a comprehensive circRNAs expression catalogue for the rat including 8 organs of both sexes during 4 developmental stages using a public RNAseq dataset. These analyses revealed thousands of circular RNA species, many expressed in an organ-specific manner along with their host genes which were enriched with tissue-specific biological functions. A large number of circRNAs also displayed a developmental-dependent expression pattern and are accumulated during ageing. CircRNAs also displayed some sexually dimorphic expression, with gender associated differences observed in various tissues and developmental stages. These observations suggest that circRNAs are dynamically expressed in a spatial-, temporal- and gender-specific manner in mammals, and may have important biological function in differentiation, development and aging.
The clinical parameters for the diagnosis of hepatitis B virus related acute-on-chronic liver failure with sepsis
Authors: Xue Ran , Zhu Yueke , Liu Hui , Meng Qinghua 
Published: February 2019

AbstractIt is still unknown that whether sepsis with hepatitis B virus related acute-on-chronic liver failure (HBV-ACLF) fit into the conventional diagnostic criteria of sepsis. Our aim was to investigate the potential clinical parameters for the diagnosis of HBV-ACLF with sepsis. A retrospective study was conducted in 43 patients with HBV-ACLF and sepsis who underwent orthotopic liver transplantation. All patients were divided into three groups according to the pathological results and laboratory test results. Immunohistochemistry (IHC) staining, hematoxylin-eosin (HE) staining and Gordon Sweet’s reticulin staining were performed in this study. Alanine aminotransferase (ALT), aspartale aminotransferase (AST), total bilirubin (TBiL), cholinesterase (CHE), albumin (ALB), prothrombin activity (PTA), blood routine examination were detected. The results being chosen at admission and before transplantation were analyzed. TBiL had a significant increase (563.5 ± 191.8 umol/L vs. 383.9 ± 157.6 umol/L, 438.3 ± 154.7 umol/L, P = 0.031) and ALT significantly decreased (81.6 ± 66.4 U/L, 754.5 ± 1084.7 U/L, 120.6 ± 102.5 U/L, P = 0.005) in sepsis group before liver transplantation. When sepsis appeared in patients with HBV-ACLF, the ratio of PLT to WBC count before liver transplantation was much lower than it at admission (4.6 ± 2.0 vs. 16.1 ± 7.2, P = 0.000). In conclusion, the clinical parameters of sepsis in patients with HBV-ACLF should be reset. The ratio of PLT/WBC and (WBCBLT/WBCAA)/ (PLTBLT/PLTAA) could remind us the occurring of sepsis in patients with HBV-ACLF.
Affective certainty and congruency of touch modulate the experience of the rubber hand illusion
Authors: Filippetti Maria Laura , Kirsch Louise P. , Crucianelli Laura , Fotopoulou Aikaterini 
Published: February 2019

AbstractOur sense of body ownership relies on integrating different sensations according to their temporal and spatial congruency. Nevertheless, there is ongoing controversy about the role of affective congruency during multisensory integration, i.e. whether the stimuli to be perceived by the different sensory channels are congruent or incongruent in terms of their affective quality. In the present study, we applied a widely used multisensory integration paradigm, the Rubber Hand Illusion, to investigate the role of affective, top-down aspects of sensory congruency between visual and tactile modalities in the sense of body ownership. In Experiment 1 (N = 36), we touched participants with either soft or rough fabrics in their unseen hand, while they watched a rubber hand been touched synchronously with the same fabric or with a ‘hidden’ fabric of ‘uncertain roughness’. In Experiment 2 (N = 50), we used the same paradigm as in Experiment 1, but replaced the ‘uncertainty’ condition with an ‘incongruent’ one, in which participants saw the rubber hand being touched with a fabric of incongruent roughness and hence opposite valence. We found that certainty (Experiment 1) and congruency (Experiment 2) between the felt and vicariously perceived tactile affectivity led to higher subjective embodiment compared to uncertainty and incongruency, respectively, irrespective of any valence effect. Our results suggest that congruency in the affective top-down aspects of sensory stimulation is important to the multisensory integration process leading to embodiment, over and above temporal and spatial properties.
Fine scale spatial variability in the influence of environmental cycles on the occurrence of dolphins at coastal sites
Authors: Fernandez-Betelu Oihane , Graham Isla M. , Cornulier Thomas , Thompson Paul M. 
Published: February 2019

AbstractEnvironmental cycles often influence the presence of animals, creating patterns at different temporal scales, which may mean that their effects overlap and/or interact. Interactions between diel and seasonal cycles have been reported to influence fish behaviour but little is known about such interactions in marine top predators. Here, we studied the combined effect of seasonal, tidal and diel cycles on the occurrence of bottlenose dolphins (Tursiops truncatus) within a Marine Protected Area in Scotland. Our analyses were based on echolocation detections from passive acoustic devices (CPODs) deployed at three coastal sites between 2010 and 2016. We described patterns of dolphins’ occurrence using circular statistics and then used generalised additive mixed models to explore the relative importance of each cycle and any interactions between them. We found site-specific cyclical patterns of presence that remained constant across years. There was a highly significant interaction between seasonal and diel cycles at two sites around deep channels, where occurrence was diurnal in summer but became nocturnal in autumn. The study demonstrates the highly plastic behaviour of bottlenose dolphins and shows a previously unreported behaviour that has management implications for this and other marine protected areas.
Application of metabolomics and molecular networking in investigating the chemical profile and antitrypanosomal activity of British bluebells (Hyacinthoides non-scripta)
Authors: Raheem Dotsha J. , Tawfike Ahmed F. , Abdelmohsen Usama R. , Edrada-Ebel RuAngelie , Fitzsimmons-Thoss Vera 
Published: February 2019

AbstractBulb, leaf, scape and flower samples of British bluebells (Hyacinthoides non-scripta) were collected regularly for one growth period. Methanolic extracts of freeze-dried and ground samples showed antitrypanosomal activity, giving more than 50% inhibition, for 20 out of 41 samples. High-resolution mass spectrometry was used in the dereplication of the methanolic extracts of the different plant parts. The results revealed differences in the chemical profile with bulb samples being distinctly different from all aerial parts. High molecular weight metabolites were more abundant in the flowers, shoots and leaves compared to smaller molecular weight ones in the bulbs. The anti-trypanosomal activity of the extracts was linked to the accumulation of high molecular weight compounds, which were matched with saponin glycosides, while triterpenoids and steroids occurred in the inactive extracts. Dereplication studies were employed to identify the significant metabolites via chemotaxonomic filtration and considering their previously reported bioactivities. Molecular networking was implemented to look for similarities in fragmentation patterns between the isolated saponin glycoside at m/z 1445.64 [M + formic-H]− equivalent to C64H104O33 and the putatively found active metabolite at m/z 1283.58 [M + formic-H]− corresponding to scillanoside L-1. A combination of metabolomics and bioactivity-guided approaches resulted in the isolation of a norlanostane-type saponin glycoside with antitrypanosomal activity of 98.9% inhibition at 20 µM.
Broadband circular polarizer for randomly polarized light in few-layer metasurface
Authors: Mun Sang-Eun , Hong Jongwoo , Yun Jeong-Geun , Lee Byoungho 
Published: February 2019

AbstractControlling the polarization state of light has been a significant issue for various integrated optical devices such as optical imaging, sensors, and communications. Recent advances in metamaterials enable the optical elements for controlling light to be miniaturized and to have various multi-functions in subwavelength scale. However, a conventional approach of a circular polarizer has an inherent limitation to eliminate the unwanted circular polarization, which means that the efficiency varies significantly depending on the polarization state of incident light. Here, we propose a novel concept of a circular polarizer by combining two functions of transmission and conversion for orthogonal circular polarizations with a total thickness of 440 nm. The proposed three-layer metasurface composed of rotating silver nanorods transmits the left-handed circularly polarized (LCP) light with maintaining its own polarization state, whereas the right-handed circularly polarized (RCP) light is converted into LCP light. Regardless of the polarization state of incoming light, the polarization of light in the last medium is LCP state in the broadband operating wavelength range from 800 nm to 1100 nm. The converted RCP and the transmitted LCP have efficiencies of up to 48.5% and 42.3%, respectively. Thus the proposed metasurface serves as a stable circular polarizer for a randomly polarized light. In addition, high-efficiency asymmetric transmission of about 0.47 is achieved at the same time due to the conversion characteristic of RCP component. The proposed metasurface has the significance as an ultra-thin optical element applicable to optical switching, sensors, and communications in unidirectional channel as well as a broadband circular polarizer for randomly polarized light.
An automated microliter-scale high-throughput screening system (MSHTS) for real-time monitoring of protein aggregation using quantum-dot nanoprobes
Authors: Sasaki Rina , Tainaka Reina , Ando Yuichi , Hashi Yurika , Deepak Hadya V. , Suga Yoshiko , Murai Yuta , Anetai Masaki , Monde Kenji , Ohta Kiminori , Ito Ikuko , Kikuchi Haruhisa , Oshima Yoshiteru , Endo Yasuyuki , Nakao Hitomi , Sakono Masafumi , Uwai Koji , Tokuraku Kiyotaka 
Published: February 2019

AbstractProtein aggregation is the principal component of numerous protein misfolding pathologies termed proteinopathies, such as Alzheimer’s disease, Parkinson’s disease, prion disease, and AA amyloidosis with unmet treatment needs. Protein aggregation inhibitors have great potential for the prevention and treatment of proteinopathies. Here we report the development of an automated real-time microliter-scale high throughput screening (MSHTS) system for amyloid aggregation inhibitors using quantum-dot nanoprobes. Screening 504 crude extracts and 134 low molecular weight aromatic compounds revealed the relationship of amyloid-β (Aβ) aggregation inhibitory activities of plant extracts using a plant-based classification. Within the eudicots, rosids, Geraniales and Myrtales showed higher activity. Screening low molecular weight aromatic compounds demonstrated that the structure of tropolone endows it with potential Aβ aggregation inhibitory activity. The activity of the most active tropolone derivative was higher than that of rosmarinic acid. MSHTS also identified three chaperone molecules as tau aggregation inhibitors. These results demonstrate that our automated MSHTS system is a novel and robust tool that can be adapted to a wide range of compounds and aggregation-prone polypeptides.
Changes in microbiome diversity following beta-lactam antibiotic treatment are associated with therapeutic versus subtherapeutic antibiotic exposure in cystic fibrosis
Authors: Hahn Andrea , Fanous Hani , Jensen Caroline , Chaney Hollis , Sami Iman , Perez Geovanny F. , Koumbourlis Anastassios C. , Louie Stan , Bost James E. , van den Anker John N. , Freishtat Robert J. , Zemanick Edith T. , Crandall Keith A. 
Published: February 2019

AbstractIn persons with cystic fibrosis (CF), decreased airway microbial diversity is associated with lower lung function. Conflicting data exist on the impact of short-term antibiotics for treatment of acute pulmonary exacerbations. However, whether differences in antibiotic exposure impacts airway microbiome changes has not been studied. We hypothesized that subtherapeutic beta-lactam antibiotic exposure, determined by the pharmacokinetics and pharmacodynamics (PK/PD) after intravenous (IV) antibiotic administration, would be associated with different patterns of changes in CF airway microbial diversity. Eligible children were enrolled when well; study assessments were performed around the time of pulmonary exacerbation. Plasma drug concentrations and bacterial minimum inhibitory concentrations (MICs) were used to determine therapeutic versus subtherapeutic beta-lactam antibiotic exposure. Respiratory samples were collected from children, and extracted bacterial DNA was amplified for the V4 region of the 16S rRNA gene. Twenty children experienced 31 APEs during the study; 45% (n = 14) of antibiotic courses were deemed therapeutic. Those in the therapeutic group had more significant decreases in alpha diversity at end of treatment and post-recovery compared to baseline than those in the subtherapeutic group. Therapeutic and subtherapeutic beta-lactam use is associated with different patterns of changes in CF airway microbial diversity following antibiotic administration.