bluuebunny/crossref_metadata_2025_split huggingface dataset:
Corrosion resistance and bioactivity enhancement of MAO coated Mg alloy depending on the time of hydrothermal treatment in Ca-EDTA solution
Authors: Kim Seo-Young , Kim Yu-Kyoung , Ryu Moon-Hee , Bae Tae-Sung , Lee Min-Ho 
Published: August 2017

AbstractIn this study, a two-step surface treatment was developed to restrain the rapid primary degradation of a biodegradable Mg alloy and to improve their biocompatibility. Micro arc oxidation (MAO) coating was performed in alkaline electrolytes such as 1.0 M NaOH with 0.1 M glycerol and 0.1 M Na3PO4. Hydrothermal treatment was performed in 0.1 M Ca-EDTA (C10H12CaN2Na2O8) and 0.5 M NaOH solution at 90 °C for different times (6, 12, 24, and 48 h). The film morphology and chemical properties were evaluated by XRD and FE-SEM. The electrochemical and corrosion behaviors were examined in the simulated body fluid, and cytotoxicity was assessed using MC3T3-E1 cells. After MAO coating, an oxide layer containing $${\bf{P}}{{\bf{O}}}_{4}^{3-}$$
P

O

4

3
−

formed on the surface. During the hydrothermal treatment in Ca-EDTA solution, calcium phosphate and Mg(OH)2 were produced via a reaction between $${\bf{P}}{{\bf{O}}}_{4}^{3-}$$
P

O

4

3
−

on the surface and Ca2+ in solution. The layer with ceramics and oxides was grown on the surface with increasing hydrothermal treatment time, and improved the surface corrosion resistance. The 24 h hydrothermal-treated group showed the lowest immersion corrosion rate and high cell viability. Therefore, this treatment was the most favorable surface modification for improving the initial corrosion resistance and bioactivity of the biodegradable Mg alloy.
Extracellular redox sensitivity of Kv1.2 potassium channels
Authors: Baronas Victoria A. , Yang Runying Y. , Kurata Harley T. 
Published: August 2017

AbstractKv1.2 is a prominent potassium channel subtype in the nervous system and serves as an important structural template for investigation of ion channel function. However, Kv1.2 voltage-dependence exhibits dramatic cell-to-cell variability due to a gating mode shift that is regulated by an unknown mechanism. We report that this variable behavior is regulated by the extracellular redox environment. Exposure to reducing agents promotes a shift in gating properties towards an ‘inhibited’ gating mode that resists opening, and causes channels to exhibit pronounced use-dependent activation during trains of repetitive depolarizations. This sensitivity to extracellular redox potential is absent in other Kv1 channels, but is apparent in heteromeric channels containing Kv1.2 subunits, and overlaps with the reported physiological range of extracellular redox couples. Mutagenesis of candidate cysteine residues fails to abolish redox sensitivity. Therefore, we suggest that an extrinsic, redox-sensitive binding partner imparts these properties.
Seasonal singing of a songbird living near the equator correlates with minimal changes in day length
Authors: Quispe Rene , Protazio João Marcelo Brazão , Gahr Manfred 
Published: August 2017

AbstractBehaving in accordance with natural cycles is essential for survival. Birds in the temperate regions use the changes of day length to time their behavior. However, at equatorial latitudes the photoperiod remains almost constant throughout the year, and it is unclear which cues songbirds use to regulate behaviors, such as singing. Here, we investigated the timing of dawn-song of male silver-beaked tanagers in the equatorial lowland Amazonas over two years. In this region, birds experience around nine minutes of annual day length variation, with sunrise times varying by 32 minutes over the year. We show that the seasonal timing of dawn-song was highly regular between years, and was strongly correlated with slight increases in day length. During the singing season the daily dawn-song onset was precisely aligned to variations in twilight time. Thus, although photoperiodic changes near the equator are minimal, songbirds can use day length variation to time singing.
Simulation of Quantum Dynamics of Excitonic Systems at Finite Temperature: an efficient method based on Thermo Field Dynamics
Authors: Borrelli Raffaele , Gelin Maxim F. 
Published: August 2017

AbstractQuantum electron-vibrational dynamics in molecular systems at finite temperature is described using an approach based on Thermo Field Dynamics theory. This formulation treats temperature effects in the Hilbert space without introducing the Liouville space. The solution of Thermo Field Dynamics equations with a novel technique for the propagation of Tensor Trains (Matrix Product States) is implemented and discussed. The methodology is applied to the study of the exciton dynamics in the Fenna-Mathews-Olsen complex using a realistic structured spectral density to model the electron-phonon interaction. The results of the simulations highlight the effect of specific vibrational modes on the exciton dynamics and energy transfer process, as well as call for careful modeling of electron-phonon couplings.
Lineage structure of Streptococcus pneumoniae may be driven by immune selection on the groEL heat-shock protein
Authors: Lourenço José , Watkins Eleanor R. , Obolski Uri , Peacock Samuel J. , Morris Callum , Maiden Martin C. J. , Gupta Sunetra 
Published: August 2017

AbstractPopulations ofStreptococcus pneumoniae(SP) are typically structured into groups of closely related organisms or lineages, but it is not clear whether they are maintained by selection or neutral processes. Here, we attempt to address this question by applying a machine learning technique to SP whole genomes. Our results indicate that lineages evolved through immune selection on the groEL chaperone protein. The groEL protein is part of thegroESLoperon and enables a large range of proteins to fold correctly within the physical environment of the nasopharynx, thereby explaining why lineage structure is so stable within SP despite high levels of genetic transfer. SP is also antigenically diverse, exhibiting a variety of distinct capsular serotypes. Associations exist between lineage and capsular serotype but these can be easily perturbed, such as by vaccination. Overall, our analyses indicate that the evolution of SP can be conceptualized as the rearrangement of modular functional units occurring on several different timescales under different pressures: some patterns have locked in early (such as the epistatic interactions betweengroESLand a constellation of other genes) and preserve the differentiation of lineages, while others (such as the associations between capsular serotype and lineage) remain in continuous flux.
Photo-flocculation of microbial mat extracellular polymeric substances and their transformation into transparent exopolymer particles: Chemical and spectroscopic evidences
Authors: Shammi Mashura , Pan Xiangliang , Mostofa Khan M. G. , Zhang Daoyong , Liu Cong-Qiang 
Published: August 2017

AbstractUpon exposure to sunlight extracellular polymeric substances (EPS) were partially transformed into transparent exopolymer particles (TEP) and unstable flocs of different sizes without the addition of any precursors. Parallel factor (PARAFAC) modelling of the sample fluorescence spectra identified humic-like and protein-like or tyrosine-like components in both untreated and irradiated EPS samples. After 58 hours of solar irradiation, humic-like substances were entirely decomposed, while the regenerated protein-like substance from EPS was the key component in the irradiated samples. Degradation and reformation of EPS occurred which was confirmed by the results of size exclusion chromatography, dissolved organic carbon, total protein and total polysaccharide analyses. Irradiated EPS was composed of –COOH or C = O (amide I band) and –NH and –CN (amide II band), while Fourier transform infrared spectroscopy (FTIR) of TEP revealed more acidic –COOH and –C–O groups, indicating typical acidic protein-like TEP. The regenerated protein-like substances could form complexes with free metals originating from degraded EPS in irradiated samples, which could be responsible for the formation of TEP/floc in the aqueous media. These results suggest that TEP/floc formation from EPS could occur by a complexation mechanism between dissolved organic matter and metals, thereby causing ionic charge neutralisation upon sunlight exposure.
Accelerating next generation sequencing data analysis with system level optimizations
Authors: Kathiresan Nagarajan , Temanni Ramzi , Almabrazi Hakeem , Syed Najeeb , Jithesh Puthen V. , Al-Ali Rashid 
Published: August 2017

AbstractNext generation sequencing (NGS) data analysis is highly compute intensive. In-memory computing, vectorization, bulk data transfer, CPU frequency scaling are some of the hardware features in the modern computing architectures. To get the best execution time and utilize these hardware features, it is necessary to tune the system level parameters before running the application. We studied the GATK-HaplotypeCaller which is part of common NGS workflows, that consume more than 43% of the total execution time. Multiple GATK 3.x versions were benchmarked and the execution time of HaplotypeCaller was optimized by various system level parameters which included: (i) tuning the parallel garbage collection and kernel shared memory to simulate in-memory computing, (ii) architecture-specific tuning in the PairHMM library for vectorization, (iii) including Java 1.8 features through GATK source code compilation and building a runtime environment for parallel sorting and bulk data transfer (iv) the default ’on-demand’ mode of CPU frequency is over-clocked by using ’performance-mode’ to accelerate the Java multi-threads. As a result, the HaplotypeCaller execution time was reduced by 82.66% in GATK 3.3 and 42.61% in GATK 3.7. Overall, the execution time of NGS pipeline was reduced to 70.60% and 34.14% for GATK 3.3 and GATK 3.7 respectively.
Evaluation of the new Chinese Disseminated Intravascular Coagulation Scoring System in critically ill patients: A multicenter prospective study
Authors: Wu Yingying , Luo Lili , Niu Ting , Han Yue , Feng Ying , Ding Qiulan , Huang Ruibin , Zhang Xiaohui , Feng Jianming , Hou Ming , Peng Jun , Li Yan , Zhou Yuhong , Su Lei , Yang Linhua , Zhou Zeping , Xue Feng , Gu Jian , Zhu Tienan , Wang Xiaomin , Deng Jun , Mei Heng , Hu Yu 
Published: August 2017

AbstractDisseminated intravascular coagulation (DIC) is a common life-threatening complication in critically ill patients. The diagnostic scoring systems of DIC enable a more prompt and accurate diagnosis of DIC, such as the International Society on Thrombosis and Haemostasis (ISTH), the Japanese Association for Acute Medicine (JAAM) and the Japanese Ministry of Health and Welfare (JMHW). This study prospectively evaluated the newly proposed Chinese DIC Scoring System (CDSS), which was conducted at 18 centers in China during a one-year period. Receiver operating characteristic (ROC) curves showed that, for diagnosis of DIC and for prediction of the 28-day all-cause mortality, the CDSS had larger areas under the ROC curve (AUCs) than the ISTH and the JAAM in different groups. The CDSS also had larger AUC than the JMHW for the ISTH DIC in non-infectious diseases. All of the AUCs of the CDSS were greater than 0.8, accompanied with both high sensitivity and high specificity. Furthermore, the CDSS score was an independent predictor of mortality (odds ratio, 1.882; p < 0.001), and could reflect the illness severity (p < 0.001 for Spearman’s rank correlations with the scores of severity). In conclusion, the CDSS is worthy of promotion with a better diagnostic and prognostic value for DIC.
Serum and urine 1H NMR-based metabolomics in the diagnosis of selected thyroid diseases
Authors: Wojtowicz Wojciech , Zabek Adam , Deja Stanislaw , Dawiskiba Tomasz , Pawelka Dorota , Glod Mateusz , Balcerzak Waldemar , Mlynarz Piotr 
Published: August 2017

AbstractEarly detection of nodular thyroid diseases including thyroid cancer is still primarily based on invasive procedures such as fine-needle aspiration biopsy. Therefore, there is a strong need for development of new diagnostic methods that could provide clinically useful information regarding thyroid nodular lesions in a non-invasive way. In this study we investigated 1H NMR based metabolic profiles of paired urine and blood serum samples, that were obtained from healthy individuals and patients with nodular thyroid diseases. Estimation of predictive potential of metabolites was evaluated using chemometric methods and revealed that both urine and serum carry information sufficient to distinguish between patients with nodular lesions and healthy individuals. Data fusion allowed to further improve prediction quality of the models. However, stratification of tumor types and their differentiation in relation to each other was not possible.
Growth differentiation factor 15 promotes blood vessel growth by stimulating cell cycle progression in repair of critical-sized calvarial defect
Authors: Wang Shaoyi , Li Mengyu , Zhang Wenjie , Hua Hongfei , Wang Ningtao , Zhao Jun , Ge Jing , Jiang Xinquan , Zhang Zhiyuan , Ye Dongxia , Yang Chi 
Published: August 2017

AbstractRepair of large bone defects remains a challenge for surgeons, tissue engineering represents a promising approach. However, the use of this technique is limited by delayed vascularization in central regions of the scaffold. Growth differentiation factor 15(GDF15) has recently been reported to be a potential angiogenic cytokine and has an ability to promote the proliferation of human umbilical vein endothelial cells(HUVECs). Whether it can be applied for promoting vascularized bone regeneration is still unknown. In this study, we demonstrated that GDF15 augmented the expression of cyclins D1 and E, induced Rb phosphorylation and E2F-1 nuclear translocation, as well as increased HUVECs proliferation. Furthermore, we also observed that GDF15 promoted the formation of functional vessels at an artificially-induced angiogenic site, and remarkably improved the healing in the repair of critical-sized calvarial defects. Our results confirm the essential role of GDF15 in angiogenesis and suggest its potential beneficial use in regenerative medicine.
Exploration of the Brain in Rest: Resting-State Functional MRI Abnormalities in Patients with Classic Galactosemia
Authors: van Erven Britt , Jansma Bernadette M. , Rubio-Gozalbo M. Estela , Timmers Inge 
Published: August 2017

AbstractPatients with classic galactosemia, a genetic metabolic disorder, encounter cognitive impairments, including motor (speech), language, and memory deficits. We used functional magnetic resonance imaging to evaluate spontaneous functional connectivity during rest to investigate potential abnormalities in neural networks. We characterized networks using seed-based correlation analysis in 13 adolescent patients and 13 matched controls. Results point towards alterations in several networks, including well-known resting-state networks (e.g. default mode, salience, visual network). Particularly, patients showed alterations in networks encompassing medial prefrontal cortex, parietal lobule and (pre)cuneus, involved in spatial orientation and attention. Furthermore, altered connectivity of networks including the insula and superior frontal gyrus -important for sensory-motor integration and motor (speech) planning- was demonstrated. Lastly, abnormalities were found in networks involving occipital regions, linked to visuospatial capacities and working memory. Importantly, across several seeds, altered functional connectivity to the superior frontal cortex, anterior insula, parietal lobule and the (pre)cuneus was observed in patients, suggesting special importance of these brain regions. Moreover, these alterations correlated with neurocognitive test results, supporting a relation with the clinical phenotype. Our findings contribute to improved characterization of brain impairments in classic galactosemia and provide directions for further investigations.
RNA-Seq analysis on chicken taste sensory organs: An ideal system to study organogenesis
Authors: Cui Xiaogang , Marshall Brett , Shi Ning , Chen Shi-You , Rekaya Romdhane , Liu Hong-Xiang 
Published: August 2017

AbstractRNA-Seq is a powerful tool in transcriptomic profiling of cells and tissues. We recently identified many more taste buds than previously appreciated in chickens using molecular markers to stain oral epithelial sheets of the palate, base of oral cavity, and posterior tongue. In this study, RNA-Seq was performed to understand the transcriptomic architecture of chicken gustatory tissues. Interestingly, taste sensation related genes and many more differentially expressed genes (DEGs) were found between the epithelium and mesenchyme in the base of oral cavity as compared to the palate and posterior tongue. Further RNA-Seq using specifically defined tissues of the base of oral cavity demonstrated that DEGs between gustatory (GE) and non-gustatory epithelium (NGE), and between GE and the underlying mesenchyme (GM) were enriched in multiple GO terms and KEGG pathways, including many biological processes. Well-known genes for taste sensation were highly expressed in the GE. Moreover, genes of signaling components important in organogenesis (Wnt, TGFβ/ BMP, FGF, Notch, SHH, Erbb) were differentially expressed between GE and GM. Combined with other features of chicken taste buds, e.g., uniquely patterned array and short turnover cycle, our data suggest that chicken gustatory tissue provides an ideal system for multidisciplinary studies, including organogenesis and regenerative medicine.
Dynamics and detection of the Newton-Wigner time delays at interfaces using a swivelling method
Authors: Floch Albert Le , Emile Olivier , Ropars Guy , Agrawal Govind P. 
Published: August 2017

AbstractEvanescent waves are ubiquitous at interfaces with optical, seismic or acoustic waves, and also with electron, neutron or atom beams. Newton was the first to suspect that both small time delays and spatial shifts exist during total internal reflection. However, these effects are so tiny that the spatial shifts were only observed in 1947 in optics, whereas the time delay values predicted by the Wigner model in the 10−14 s range in optics had to await femtosecond lasers to be detected with difficulty. The spatial shifts have been isolated in many areas but the time delays, though fundamental, generally remain out of reach, particularly with particles. In textbooks usually both quantities are supposed to be simply linked. Here we report, using swivelling detectors, that the spatial and temporal measurements are intimately intermingled, especially in the so-called cyclical regime. Indeed, while the spatial shift does not depend on the type of detection, the measured time delay can be positive, negative or zero, but controllable. We also discuss how such intricate measurements of spatial and temporal effects allow crucial time penalties to be eliminated in guided soliton propagation, and should be used to unambiguously identify the Newton-Wigner time delays for particles.
RNA-Seq reveals MicroRNA expression signature and genetic polymorphism associated with growth and muscle quality traits in rainbow trout
Authors: Paneru Bam Dev , Al-Tobasei Rafet , Kenney Brett , Leeds Timothy D. , Salem Mohamed 
Published: August 2017

AbstractThe role of microRNA expression and genetic variation in microRNA-binding sites of target genes on growth and muscle quality traits is poorly characterized. We used RNA-Seq approach to investigate their importance on 5 growth and muscle quality traits: whole body weight (WBW), muscle yield, muscle crude-fat content, muscle shear force and whiteness. Phenotypic data were collected from 471 fish, representing 98 families (~5 fish/family) from a growth-selected line. Muscle microRNAs and mRNAs were sequenced from 22 families showing divergent phenotypes. Ninety microRNAs showed differential expression between families with divergent phenotypes, and their expression was strongly associated with variation in phenotypes. A total of 204 single nucleotide polymorphisms (SNPs) present in 3′ UTR of target genes either destroyed or created novel illegitimate microRNA target sites; of them, 78 SNPs explained significant variation in the aforementioned 5 muscle traits. Majority of the phenotype-associated SNPs were present in microRNA-binding sites of genes involved in energy metabolism and muscle structure. These findings suggest that variation in microRNA expression and/or sequence variation in microRNA binding sites in target genes play an important role in mediating differences in fish growth and muscle quality phenotypes.
GBF3 transcription factor imparts drought tolerance in Arabidopsis thaliana
Authors: Ramegowda Venkategowda , Gill Upinder Singh , Sivalingam Palaiyur Nanjappan , Gupta Aarti , Gupta Chirag , Govind Geetha , Nataraja Karaba N. , Pereira Andy , Udayakumar Makarla , Mysore Kirankumar S. , Senthil-Kumar Muthappa 
Published: August 2017

AbstractDrought transcriptome analysis of finger millet (Eleusine coracana) by cDNA subtraction identified drought responsive genes that have a potential role in drought tolerance. Through virus-induced gene silencing (VIGS) in a related crop species, maize (Zea mays), several genes, including a G-BOX BINDING FACTOR 3 (GBF3) were identified as candidate drought stress response genes and the role of GBF3 in drought tolerance was studied in Arabidopsis thaliana. Overexpression of both EcGBF3 and AtGBF3 in A. thaliana resulted in improved tolerance to osmotic stress, salinity and drought stress in addition to conferring insensitivity to ABA. Conversely, loss of function of this gene increased the sensitivity of A. thaliana plants to drought stress. EcGBF3 transgenic A. thaliana results also suggest that drought tolerance of sensitive plants can be improved by transferring genes from far related crops like finger millet. Our results demonstrate the role of GBF3 in imparting drought tolerance in A. thaliana and indicate the conserved role of this gene in drought and other abiotic stress tolerance in several plant species.
Naturally acquired antibody response to Plasmodium falciparum describes heterogeneity in transmission on islands in Lake Victoria
Authors: Idris Zulkarnain Md , Chan Chim W. , Kongere James , Hall Tom , Logedi John , Gitaka Jesse , Drakeley Chris , Kaneko Akira 
Published: August 2017

AbstractAs markers of exposure anti-malaria antibody responses can help characterise heterogeneity in malaria transmission. In the present study antibody responses to Plasmodium falciparum AMA-1, MSP-119 and CSP were measured with the aim to describe transmission patterns in meso-endemic settings in Lake Victoria. Two cross-sectional surveys were conducted in Lake Victoria in January and August 2012. The study area comprised of three settings: mainland (Ungoye), large island (Mfangano) and small islands (Takawiri, Kibuogi, Ngodhe). Individuals provided a finger-blood sample to assess malaria infection by microscopy and PCR. Antibody response to P. falciparum was determined in 4,112 individuals by ELISA using eluted dried blood from filter paper. The overall seroprevalence was 64.0% for AMA-1, 39.5% for MSP-119, and 12.9% for CSP. Between settings, seroprevalences for merozoite antigens were similar between Ungoye and Mfangano, but higher when compared to the small islands. For AMA-1, the seroconversion rates (SCRs) ranged from 0.121 (Ngodhe) to 0.202 (Ungoye), and were strongly correlated to parasite prevalence. We observed heterogeneity in serological indices across study sites in Lake Victoria. These data suggest that AMA-1 and MSP-119 sero-epidemiological analysis may provide further evidence in assessing variation in malaria exposure and evaluating malaria control efforts in high endemic area.