bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential miRNA expression in the three-spined stickleback, response to environmental changes
Authors: Rastorguev S. M. , Nedoluzhko A. V. , Gruzdeva N. M. , Boulygina E. S. , Sharko F. S. , Ibragimova A. S. , Tsygankova S. V. , Artemov A. V. , Skryabin K. G. , Prokhortchouk E. B. 
Published: December 2017

AbstractmiRNAs play important role in the various physiological and evolutionary processes, however, there is no data allowing comparison of evolutionary differences between various ecotypes adapted to different environmental conditions and specimen demonstrating immediate physiological response to the environmental changes. We compared miRNA expression profiles between marine and freshwater stickleback populations of the three-spined stickleback to identify the evolutionary differences. To study the immediate physiological response to foreign environment, we explored the changes induced by transfer of marine sticklebacks into freshwater environment and vice versa. Comparative analysis of changes in miRNA expression suggested that they are driven by three independent factors: (1) non-specific changes in miRNA expression under different environmental conditions; (2) specific response to freshwater conditions in the marine stickleback ecotype; (3) specific response to extreme osmotic conditions for both marine and freshwater ecotypes during the contact with non-native environment. Gene Ontology enrichment analysis of differential expressed miRNA targets supports our current hypothesis.
Topographical diversity of common skin microflora and its association with skin environment type: An observational study in Chinese women
Authors: Li Xi , Yuan Chao , Xing Licong , Humbert Philippe 
Published: December 2017

AbstractThis study evaluated cutaneous microbial distribution, and microbial co-occurrence at different body sites and skin environments in Chinese women (39.6 ± 11.9 years, N = 100) during the winter season. Microbial distribution (Propionibacterium acnes, Staphylococcus aureus, Staphylococcus epidermidis, Lactobacillus, Pseudomonadaceae, and Malassezia furfur), association with biomarkers (antimicrobial peptides: LL-37, β-defensins [HBD-2, HBD-3]), and claudin-1) and skin biophysical parameters (transepidermal water loss, pH, skin scaliness and roughness, sebum and hydration levels) were also determined. Skin sites (glabella [GL], hand-back [HB], interdigital web-space [IS], antecubital fossa [AF], volar forearm [VF], back [BA]) were classified as normal, oily or dry based on two-step cluster analysis and exposed or unexposed (uncovered or covered by clothes, respectively) based on seasonal apparel. Pseudomonadaceae and Staphylococcus aureus had the highest and lowest detection rate respectively at all sites. Cluster analysis identified skin sites as ‘normal’ (HB, BA, AF, VF), ‘dry’ (IS) and ‘oily’ (GL). Bacterial alpha diversity was higher in exposed (HB, IS, and GL) compared with unexposed sites (BA, AF and VF). Co-occurrence of Staphylococcus aureus with any of the other five microorganisms was lower in dry and oily skin versus normal skin. Skin exposure, biophysical/barrier profile and biomarkers were found to be associated with bacterial distribution and co-occurrence.
LUCS (Light-Up Cell System), a universal high throughput assay for homeostasis evaluation in live cells
Authors: Derick Sylvain , Gironde Camille , Perio Pierre , Reybier Karine , Nepveu Françoise , Jauneau Alain , Furger Christophe 
Published: December 2017

AbstractObservations of fluorescent cyanine dye behavior under illumination at 500 nm lead to a novel concept in cell biology allowing the development of a new live cell assay called LUCS, for Light-Up Cell System, measuring homeostasis in live cells. Optimization of the LUCS process resulted in a standardized, straightforward and high throughput assay with applications in toxicity assessment. The mechanisms of the LUCS process were investigated. Electron Paramagnetic Resonance experiments showed that the singlet oxygen and hydroxyl radical are involved downstream of the light effect, presumably leading to deleterious oxidative stress that massively opens access of the dye to its intracellular target. Reversible modulation of LUCS by both verapamil and proton availability indicated that plasma membrane proton/cation antiporters, possibly of the MATE drug efflux transport family, are involved. A mechanistic model is presented. Our data show that intracellular oxidation can be controlled by tuning light energy, opening applications in regulatory purposes, anti-oxidant research, chemotherapy efficacy and dynamic phototherapy strategies.
Lack of acclimatization to chronic hypoxia in humans in the Antarctica
Authors: Porcelli Simone , Marzorati Mauro , Healey Beth , Terraneo Laura , Vezzoli Alessandra , Bella Silvia Della , Dicasillati Roberto , Samaja Michele 
Published: December 2017

AbstractThe study was carried out at Concordia Station (Antarctic Plateau). The aim was to investigate the respiratory and haematological responses to hypoxia in healthy subjects living at constant altitude. Thirteen men and women (34.1 ± 3.1 years) were exposed for 10 months to hypobaric hypoxia (oxygen level equivalent to 3800 m asl). These unique conditions enable a greater accuracy of monitoring human responses to chronic hypoxia than can be achieved elsewhere. Blood haemoglobin and erythropoietin concentrations were determined at sea level (Pre), and after 3, 7, 20, 90 and 300 days at altitude. Blood gas analysis, base excess and arterial oxygen saturation were measured at Pre, and after 150 and 300 days at altitude. Erythropoietin returned quickly to baseline level after a transient increase in the first days. Blood haemoglobin concentration started increasing at day 7 and remained markedly higher for the entire duration of the mission. At day 150 the blood carbon dioxide partial pressure was markedly reduced, and consequently blood pH remained higher at negative base excess until day 300. The arterial oxygen saturation remained lower than Pre throughout. In conclusion, humans display little capacity of hypoxia acclimatization even after ten months of constant exposure to low oxygen partial pressure.
Quantitative predictions of diverse wrinkling patterns in film/substrate systems
Authors: Xu Fan , Potier-Ferry Michel 
Published: December 2017

AbstractA basic characteristic of stiff film/soft substrate systems is their ability to experience large deformation under compressive stresses, which inevitably leads to formation of patterns on the surface. Such pattern formation is the result of loss of stability and symmetry breaking. Knowledge on how such instabilities arise and evolve is essential to describe, understand, predict, and ultimately to design complex functional materials and structures, for example the fabrication of stretchable electronic devices and micro/nano-scale surface patterning control. In this paper, quantitative predictions of various instability pattern formations and evolutions, which involve highly nonlinear deformation and multiple bifurcations, will be presented based on advanced mechanical models and methods, from planar to curved geometry. The results can provide further insight into fundamental understanding in a whole view of a variety of surface patterning morphology and imply a potential way to facilitate the design of functional materials and structures by quantitatively harnessing surface instabilities.
Orientation in Virtual Reality Does Not Fully Measure Up to the Real-World
Authors: Kimura Kazushige , Reichert James F. , Olson Ashley , Pouya Omid Ranjbar , Wang Xikui , Moussavi Zahra , Kelly Debbie M. 
Published: December 2017

AbstractAdult participants learned to reorient to a specific corner inside either a real or virtual rectangular room containing a distinct featural object in each corner. Participants in the virtual-reality (VR) condition experienced an immersive virtual version of the physical room using a head-mounted display (HMD) and customized manual wheelchair to provide self-movement. Following a disorientation procedure, people could reorient by using either the geometry of the room and/or the distinct features in the corners. Test trials in which the different spatial cues were manipulated revealed participants encoded features and geometry in both the real and VR rooms. However, participants in the VR room showed less facility with using geometry. Our results suggest caution must be taken when interpreting the nuances of spatial cue use in virtual environments. Reduced reliability of geometric cues in VR environments may result in greater reliance on feature cues than would normally be expected under similar real-world conditions.
Hierarchical Porous Chitosan Sponges as Robust and Recyclable Adsorbents for Anionic Dye Adsorption
Authors: Wang Mei , Ma Yifei , Sun Yan , Hong Sung Yong , Lee Stephanie K. , Yoon Bumyong , Chen Long , Ci Lijie , Nam Jae-Do , Chen Xuyuan , Suhr Jonghwan 
Published: December 2017

AbstractBiomass waste treatment and detrimental dye adsorption are two of the crucial environmental issues nowadays. In this study, we investigate to simultaneously resolve the aforementioned issues by synthesizing chitosan sponges as adsorbents toward rose bengal (RB) dye adsorption. Through a temperature-controlled freeze-casting process, robust and recyclable chitosan sponges are fabricated with hierarchical porosities resulted from the control of concentrations of chitosan solutions. Tested as the adsorbents for RB, to the best of our knowledge, the as-prepared chitosan sponge in this work reports the highest adsorption capacity of RB (601.5 mg/g) ever. The adsorption mechanism, isotherm, kinetics, and thermodynamics are comprehensively studied by employing statistical analysis. Importantly and desirably, the sponge type of chitosan adsorbents exceedingly facilitates the retrieving and elution of chitosan sponges for recyclable uses. Therefore, the chitosan sponge adsorbent is demonstrated to possess dramatically squeezable capability with durability for 10,000 cycles and recyclable adsorption for at least 10 cycles, which provides an efficient and economical way for both biomass treatment and water purification.
Diagnosis and typing of influenza using fluorescent barcoded probes
Authors: Huang Bixing , West Nicholas P. , Vider Jelena , Cox Amanda J. , Constantino Tanya , Harrower Bruce J. , Pyke Alyssa T. , McMahon Jamie , Northill Judith A. , Riordan Tim , Warrilow David 
Published: December 2017

AbstractIn this work, we explore a new hybridization technology using barcoded probes which has large-scale multiplexing capability. We used influenza virus to test whether the technology has application in virus diagnostics. Typing of influenza virus strains is an important aspect of global health surveillance. Standard typing procedures use serological or amplification-based assays performed sequentially. By comparison, the hybridization technology was correctly able to detect, type and subtype influenza A and B virus strains directly from clinical samples in a single reaction without prior virus isolation or amplification. Whilst currently not as sensitive as amplification-based assays, these results are a first-step towards application of this technology to the detection and typing of influenza and other viruses.
Resequencing of the Leishmania infantum (strain JPCM5) genome and de novo assembly into 36 contigs
Authors: González-de la Fuente Sandra , Peiró-Pastor Ramón , Rastrojo Alberto , Moreno Javier , Carrasco-Ramiro Fernando , Requena Jose M. , Aguado Begoña 
Published: December 2017

AbstractLeishmania parasites are the causative of leishmaniasis, a group of potentially fatal human diseases. Control strategies for leishmaniasis can be enhanced by genome based investigations. The publication in 2005 of the Leishmania major genome sequence, and two years later the genomes for the species Leishmania braziliensis and Leishmania infantum were major milestones. Since then, the L. infantum genome, although highly fragmented and incomplete, has been used widely as the reference genome to address whole transcriptomics and proteomics studies. Here, we report the sequencing of the L. infantum genome by two NGS methodologies and, as a result, the complete genome assembly on 36 contigs (chromosomes). Regarding the present L. infantum genome-draft, 495 new genes have been annotated, a hundred have been corrected and 75 previous annotated genes have been discontinued. These changes are not only the result of an increase in the genome size, but a significant contribution derives from the existence of a large number of incorrectly assembled regions in current chromosomal scaffolds. Furthermore, an improved assembly of tandemly repeated genes has been obtained. All these analyses support that the de novo assembled L. infantum genome represents a robust assembly and should replace the currently available in the databases.
The interaction of fat mass and obesity associated gene polymorphisms and dietary fiber intake in relation to obesity phenotypes
Authors: Hosseini-Esfahani Firoozeh , Koochakpoor Gelareh , Daneshpour Maryam S. , Mirmiran Parvin , Sedaghati-khayat Bahareh , Azizi Fereidoun 
Published: December 2017

AbstractControversies surrounding the effectiveness of fiber intake for prevention of obesity can be attributed to differences in the genetic makeup of individuals. This study aims to examining the interaction between dietary fiber intake and common fat mass and obesity–associated (FTO) single-nucleotide polymorphisms (SNPs), in relation to obesity. Subjects of this nested case-control study were selected from among adult participants of the Tehran Lipid and Glucose Study. Cases (n = 627) were individually matched with controls, who had normal weight. Six selected SNPs (rs1421085, rs1121980, rs17817449, rs8050136, rs9939973, and rs3751812) were genotyped by tetra-refractory mutation system-polymerase chain reaction analysis. Genetic risk scores (GRS) were calculated using the weighted method. A significant interaction was observed between total fiber intake and the GRS in relation to obesity (Pinteraction = 0.01); the difference in the risk for obesity was more pronounced in individuals with GRS ≥ 6 who consumed ≥ 14 grams of fiber a day (OR: 2.74, CI: 2.40–3.35 vs Ref.; P trend = 0.0005) than in individuals with GRS < 6 (P trend = 0.34). Dietary fiber intakes modified the association of FTO SNPs and the GRS with general obesity, an effect which was more pronounced in those who consumed high levels of dietary fiber and had a high number of risk alleles.
Developing and diagnosing climate change indicators of regional aerosol optical properties
Authors: Sullivan Ryan C. , Levy Robert C. , da Silva Arlindo M. , Pryor Sara C. 
Published: December 2017

AbstractGiven the importance of aerosol particles to radiative transfer via aerosol-radiation interactions, a methodology for tracking and diagnosing causes of temporal changes in regional-scale aerosol populations is illustrated. The aerosol optical properties tracked include estimates of total columnar burden (aerosol optical depth, AOD), dominant size mode (Ångström exponent, AE), and relative magnitude of radiation scattering versus absorption (single scattering albedo, SSA), along with metrics of the structure of the spatial field of these properties. Over well-defined regions of North America, there are generally negative temporal trends in mean and extreme AOD, and SSA. These are consistent with lower aerosol burdens and transition towards a relatively absorbing aerosol, driven primarily by declining sulfur dioxide emissions. Conversely, more remote regions are characterized by increasing mean and extreme AOD that is attributed to increased local wildfire emissions and long-range (transcontinental) transport. Regional and national reductions in anthropogenic emissions of aerosol precursors are leading to declining spatial autocorrelation in the aerosol fields and increased importance of local anthropogenic emissions in dictating aerosol burdens. However, synoptic types associated with high aerosol burdens are intensifying (becoming more warm and humid), and thus changes in synoptic meteorology may be offsetting aerosol burden reductions associated with emissions legislation.
Ferromagnetic Phase in Nonequilibrium Quantum Dots
Authors: Hou WenJie , Wang YuanDong , Wei JianHua , Yan YiJing 
Published: December 2017

AbstractBy nonperturbatively solving the nonequilibrium Anderson two-impurity model with the hierarchical equations of motion approach, we report a robust ferromagnetic (FM) phase in series-coupled double quantum dots, which can suppress the antiferromagnetic (AFM) phase and dominate the phase diagram at finite bias and detuning energy in the strongly correlated limit. The FM exchange interaction origins from the passive parallel spin arrangement caused by the Pauli exclusion principle during the electrons transport. At very low temperature, the Kondo screening of the magnetic moment in the FM phase induces some nonequilibrium Kondo effects in magnetic susceptibility, spectral functions and current. In the weakly correlated limit, the AFM phase is found still stable, therefore, a magnetic-field-free internal control of spin states can be expected through the continuous FM–AFM phase transition.
Entropy is a Simple Measure of the Antibody Profile and is an Indicator of Health Status: A Proof of Concept
Authors: Wang Lu , Whittemore Kurt , Johnston Stephen Albert , Stafford Phillip 
Published: December 2017

AbstractWe have previously shown that the diversity of antibodies in an individual can be displayed on chips on which 130,000 peptides chosen from random sequence space have been synthesized. This immunosignature technology is unbiased in displaying antibody diversity relative to natural sequence space, and has been shown to have diagnostic and prognostic potential for a wide variety of diseases and vaccines. Here we show that a global measure such as Shannon’s entropy can be calculated for each immunosignature. The immune entropy was measured across a diverse set of 800 people and in 5 individuals over 3 months. The immune entropy is affected by some population characteristics and varies widely across individuals. We find that people with infections or breast cancer, generally have higher entropy values than non-diseased individuals. We propose that the immune entropy as measured from immunosignatures may be a simple method to monitor health in individuals and populations.
Residues His172 and Lys238 are Essential for the Catalytic Activity of the Maleylacetate Reductase from Sphingobium chlorophenolicum Strain L-1
Authors: Chen Lifeng , Krol Ed S. , Sakharkar Meena K. , Khan Haseeb A. , Alhomida Abdullah S. , Yang Jian 
Published: December 2017

AbstractMaleylacetate reductase (PcpE), the last enzyme in the pentachlorophenol biodegradation pathway in Sphingobium chlorophenolicum L-1, catalyzes two consecutive reductive reactions, reductive dehalogenation of 2-chloromaleylacetate (2-CMA) to maleylacetate (MA) and subsequent reduction of MA to 3-oxoadipate (3-OXO). In each reaction, one molecule of NADH is consumed. To better understand its catalytic function, we undertook a structural model-based site-directed mutagenesis and steady-state kinetics study of PcpE. Our results showed that the putative catalytic site of PcpE is located in a positively charged solvent channel at the interface of the two domains and the binding of 2-CMA/MA involves seven basic amino acids, His172, His236, His237, His241 and His251, Lys140 and Lys238. Mutagenesis studies showed that His172 and Lys238 are essential for the catalytic activity of PcpE. However, the mutation of His236 to an alanine can increase the catalytic efficiency (k
cat
/K
m
) of PcpE by more than 2-fold, implying that PcpE is still in an early stage of molecular evolution. Similar to tetrachlorobenzoquinone reductase (PcpD), PcpE is also inhibited by pentachlorophenol in a concentration-dependent manner. Furthermore, our studies showed that PcpE exhibits an extremely low but detectable level of alcohol dehalogenase activity toward ethanol and supports the notion that it is evolved from an iron-containing alcohol dehydrogenase.
Hydrothermal transformation of SnSe crystal to Se nanorods in oxalic acid solution and the outstanding thermoelectric power factor of Se/SnSe composite
Authors: Ju Hyun , Park Dabin , Kim Jooheon 
Published: December 2017

AbstractThe present work demonstrates the synthesis of one-dimensional (1D) Se nanorods with ~50 nm diameter by hydrothermal transformation of SnSe crystals in oxalic acid solution and suggests the reaction mechanism for this chemical transformation. SnSe particles react with oxalic acid to generate numerous Se nuclei, which crystallize into Se nanorods due to the intrinsic character of the 1D growth of Se. The resulting Se/SnSe composite exhibits outstanding thermoelectric power factor without the aid of any rare dopants, which is higher than both undoped polycrystalline SnSe and SnSe doped with Pb and Cu.
PCA-based approach for subtracting thermal background emission in high-contrast imaging data
Authors: Hunziker S. , Quanz S. P. , Amara A. , Meyer M. R. 
Published: December 2017

Aims.Ground-based observations at thermal infrared wavelengths suffer from large background radiation due to the sky, telescope and warm surfaces in the instrument. This significantly limits the sensitivity of ground-based observations at wavelengths longer than ~3 μm. The main purpose of this work is to analyse this background emission in infrared high-contrast imaging data as illustrative of the problem, show how it can be modelled and subtracted and demonstrate that it can improve the detection of faint sources, such as exoplanets.
Methods. We used principal component analysis (PCA) to model and subtract the thermal background emission in three archival high-contrast angular differential imaging datasets in the M′ and L′ filter. We used an M′ dataset of β Pic to describe in detail how the algorithm works and explain how it can be applied. The results of the background subtraction are compared to the results from a conventional mean background subtraction scheme applied to the same dataset. Finally, both methods for background subtraction are compared by performing complete data reductions. We analysed the results from the M′ dataset of HD 100546 only qualitatively. For the M′ band dataset of β Pic and the L′ band dataset of HD 169142, which was obtained with an angular groove phase mask vortex vector coronagraph, we also calculated and analysed the achieved signal-to-noise ratio (S/N).
Results. We show that applying PCA is an effective way to remove spatially and temporarily varying thermal background emission down to close to the background limit. The procedure also proves to be very successful at reconstructing the background that is hidden behind the point spread function. In the complete data reductions, we find at least qualitative improvements for HD 100546 and HD 169142, however, we fail to find a significant increase in S/N of β Pic b. We discuss these findings and argue that in particular datasets with strongly varying observing conditions or infrequently sampled sky background will benefit from the new approach.