bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intricate disorder in defect fluorite/pyrochlore: a concord of chemistry and crystallography
Authors: Simeone David , Thorogood Gordon James , Huo Da , Luneville Laurence , Baldinozzi Gianguido , Petricek Vaclav , Porcher Florence , Ribis Joel , Mazerolles Leo , Largeau Ludovic , Berar Jean Francois , Surble Suzy 
Published: June 2017

AbstractIntuitively scientists accept that order can emerge from disorder and a significant amount of effort has been devoted over many years to demonstrate this. In metallic alloys and oxides, disorder at the atomic scale is the result of occupation at equivalent atomic positions by different atoms which leads to the material exhibiting a fully random or modulated scattering pattern. This arrangement has a substantial influence on the material’s properties, for example ionic conductivity. However it is generally accepted that oxides, such as defect fluorite as used for nuclear waste immobilization matrices and fuel cells, are the result of disorder at the atomic scale. To investigate how order at the atomic scale induces disorder at a larger scale length, we have applied different techniques to study the atomic composition of a homogeneous La2Zr2O7 pyrochlore, a textbook example of such a structure. Here we demonstrate that a pyrochlore, which is considered to be defect fluorite, is the result of intricate disorder due to a random distribution of fully ordered nano-domains. Our investigation provides new insight into the order disorder transformations in complex materials with regards to domain formation, resulting in a concord of chemistry with crystallography illustrating that order can induce disorder.
The role of PTEN - HCV core interaction in hepatitis C virus replication
Authors: Wu Qi , Li Zhubing , Mellor Paul , Zhou Yan , Anderson Deborah H. , Liu Qiang 
Published: June 2017

AbstractHepatitis C virus (HCV) infection leads to severe liver diseases including hepatocellular carcinoma (HCC). Phosphatase and tensin homolog deleted on chromosome 10 (PTEN), a tumour suppressor, is frequently mutated or deleted in HCC tumors. PTEN has previously been demonstrated to inhibit HCV secretion. In this study, we determined the effects of PTEN on the other steps in HCV life cycle, including entry, translation, and replication. We showed that PTEN inhibits HCV entry through its lipid phosphatase activity. PTEN has no effect on HCV RNA translation. PTEN decreases HCV replication and the protein phosphatase activity of PTEN is essential for this function. PTEN interacts with the HCV core protein and requires R50 in domain I of HCV core and PTEN residues 1–185 for this interaction. This interaction is required for PTEN-mediated inhibition of HCV replication. This gives rise to a reduction in PTEN levels and intracellular lipid abundance, which may in turn regulate HCV replication. HCV core domain I protein increases the lipid phosphatase activity of PTEN in an in vitro assay, suggesting that HCV infection can also regulate PTEN. Taken together, our results demonstrated an important regulatory role of PTEN in the HCV life cycle.
Seabirds supply nitrogen to reef-building corals on remote Pacific islets
Authors: Lorrain Anne , Houlbrèque Fanny , Benzoni Francesca , Barjon Lucie , Tremblay-Boyer Laura , Menkes Christophe , Gillikin David P. , Payri Claude , Jourdan Hervé , Boussarie Germain , Verheyden Anouk , Vidal Eric 
Published: June 2017

AbstractSeabirds concentrate nutrients from large marine areas on their nesting islands playing an important ecological role in nutrient transfer between marine and terrestrial ecosystems. Here we investigate the role of guano on corals reefs across scales by analyzing the stable nitrogen isotopic (δ15N) values of the scleractinian coralPocillopora damicornison fringing reefs around two Pacific remote islets with large seabird colonies. Marine stations closest to the seabird colonies had higher nitrate + nitrite concentrations compared to more distant stations. Coral and zooxanthellae δ15N values were also higher at these sites, suggesting that guano-derived nitrogen is assimilated into corals and contributes to their nitrogen requirements. The spatial extent of guano influence was however restricted to a local scale. Our results demonstrate that seabird-derived nutrients not only spread across the terrestrial ecosystem, but also affect components of the adjacent marine ecosystem. Further studies are now needed to assess if this nutrient input has a positive or negative effect for corals. Such studies on remote islets also open fresh perspectives to understand how nutrients affect coral reefs isolated from other anthropogenic stressors.
Exendin-4 attenuates blast traumatic brain injury induced cognitive impairments, losses of synaptophysin and in vitro TBI-induced hippocampal cellular degeneration
Authors: Rachmany Lital , Tweedie David , Rubovitch Vardit , Li Yazhou , Holloway Harold W. , Kim Dong Seok , Ratliff Whitney A. , Saykally Jessica N. , Citron Bruce A. , Hoffer Barry J. , Greig Nigel H. , Pick Chaim G. 
Published: June 2017

AbstractMild blast traumatic brain injury (B-TBI) induced lasting cognitive impairments in novel object recognition and less severe deficits in Y-maze behaviors. B-TBI significantly reduced the levels of synaptophysin (SYP) protein staining in cortical (CTX) and hippocampal (HIPP) tissues. Treatment with exendin-4 (Ex-4) delivered by subcutaneous micro-osmotic pumps 48 hours prior to or 2 hours immediately after B-TBI prevented the induction of both cognitive deficits and B-TBI induced changes in SYP staining. The effects of a series of biaxial stretch injuries (BSI) on a neuronal derived cell line, HT22 cells, were assessed in an in vitro model of TBI. Biaxial stretch damage induced shrunken neurites and cell death. Treatment of HT22 cultures with Ex-4 (25 to 100 nM), prior to injury, attenuated the cytotoxic effects of BSI and preserved neurite length similar to sham treated cells. These data imply that treatment with Ex-4 may represent a viable option for the management of secondary events triggered by blast-induced, mild traumatic brain injury that is commonly observed in militarized zones.
Optimal angle of magnetic field for magnetic bubblecade motion
Authors: Kim Duck-Ho , Moon Kyoung-Woong , Yoo Sang-Cheol , Kim Dae-Yun , Min Byoung-Chul , Hwang Chanyong , Choe Sug-Bong 
Published: June 2017

AbstractUnidirectional motion of magnetic structures such as the magnetic domain and domain walls is a key concept underlying next-generation memory and logic devices. As a potential candidate of such unidirectional motion, it has been recently demonstrated that the magnetic bubblecade—the coherent unidirectional motion of magnetic bubbles—can be generated by applying an alternating magnetic field. Here we report the optimal configuration of applied magnetic field for the magnetic bubblecade. The tilted alternating magnetic field induces asymmetric expansion and shrinkage of the magnetic bubbles under the influence of the Dzyaloshinskii-Moriya interaction, resulting in continuous shift of the bubbles in time. By examining the magnetic bubblecade in Pt/Co/Pt films, we find that the bubblecade speed is sensitive to the tilt angle with a maximum at an angle, which can be explained well by a simple analytical form within the context of the domain-wall creep theory. A simplified analytic formula for the angle for maximum speed is then given as a function of the amplitude of the alternating magnetic field. The present results provide a useful guideline of optimal design for magnetic bubblecade memory and logic devices.
Quantitative modelling of hip fracture trends in 14 European countries: testing variations of a shared reversal over time
Authors: Lucas Raquel , Martins Ana , Severo Milton , Silva Poliana , Monjardino Teresa , Gaio Ana Rita , Cooper Cyrus , Barros Henrique 
Published: June 2017

AbstractQualitative similarities between hip fracture trends in different countries suggests variations of the same epidemic. We tested a single statistical shape to describe time trends in Europe, while allowing for country-level variability. Using data from 14 countries, we modelled incidence rates over time using linear mixed-effects models, including the fixed effects of calendar year and age. Random effects were tested to quantify country-level variability in background rates, timing of trend reversal and tempo of reversal. Mixture models were applied to identify clusters of countries defined by common behavioural features. A quadratic function of time, with random effects for background rates and timing of trend reversal, adjusted well to the observed data. Predicted trend reversal occurred on average in 1999 in women (peak incidence about 600 per 100 000) and 2000 in men (about 300 per 100 000). Mixture modelling of country-level effects suggested three clusters for women and two for men. In both sexes, Scandinavia showed higher rates but earlier trend reversals, whereas later trend reversals but lower peak incidences were found in Southern Europe and most of Central Europe. Our finding of a similar overall reversal pattern suggests that different countries show variations of a shared hip fracture epidemic.
Probing spermiogenesis: a digital strategy for mouse acrosome classification
Authors: Taloni Alessandro , Font-Clos Francesc , Guidetti Luca , Milan Simone , Ascagni Miriam , Vasco Chiara , Pasini Maria Enrica , Gioria Maria Rosa , Ciusani Emilio , Zapperi Stefano , La Porta Caterina A. M. 
Published: June 2017

AbstractClassification of morphological features in biological samples is usually performed by a trained eye but the increasing amount of available digital images calls for semi-automatic classification techniques. Here we explore this possibility in the context of acrosome morphological analysis during spermiogenesis. Our method combines feature extraction from three dimensional reconstruction of confocal images with principal component analysis and machine learning. The method could be particularly useful in cases where the amount of data does not allow for a direct inspection by trained eye.
Data-driven nanomechanical sensing: specific information extraction from a complex system
Authors: Shiba Kota , Tamura Ryo , Imamura Gaku , Yoshikawa Genki 
Published: June 2017

AbstractSmells are known to be composed of thousands of chemicals with various concentrations, and thus, the extraction of specific information from such a complex system is still challenging. Herein, we report for the first time that the nanomechanical sensing combined with machine learning realizes the specific information extraction, e.g. alcohol content quantification as a proof-of-concept, from the smells of liquors. A newly developed nanomechanical sensor platform, a Membrane-type Surface stress Sensor (MSS), was utilized. Each MSS channel was coated with functional nanoparticles, covering diverse analytes. The smells of 35 liquid samples including water, teas, liquors, and water/EtOH mixtures were measured using the functionalized MSS array. We selected characteristic features from the measured responses and kernel ridge regression was used to predict the alcohol content of the samples, resulting in successful alcohol content quantification. Moreover, the present approach provided a guideline to improve the quantification accuracy; hydrophobic coating materials worked more effectively than hydrophilic ones. On the basis of the guideline, we experimentally demonstrated that additional materials, such as hydrophobic polymers, led to much better prediction accuracy. The applicability of this data-driven nanomechanical sensing is not limited to the alcohol content quantification but to various fields including food, security, environment, and medicine.
Looking beyond the imaging plane: 3D needle tracking with a linear array ultrasound probe
Authors: Xia Wenfeng , West Simeon J. , Finlay Malcolm C. , Mari Jean-Martial , Ourselin Sebastien , David Anna L. , Desjardins Adrien E. 
Published: June 2017

AbstractUltrasound is well suited for guiding many minimally invasive procedures, but its use is often precluded by the poor visibility of medical devices. When devices are not visible, they can damage critical structures, with life-threatening complications. Here, we developed the first ultrasound probe that comprises both focused and unfocused transducer elements to provide both 2D B-mode ultrasound imaging and 3D ultrasonic needle tracking. A fibre-optic hydrophone was integrated into a needle to receive Golay-coded transmissions from the probe and these data were processed to obtain tracking images of the needle tip. The measured tracking accuracy in water was better than 0.4 mm in all dimensions. To demonstrate the clinical potential of this system, insertions were performed into the spine and the uterine cavity, in swine and pregnant ovine models in vivo. In both models, the SNR ranged from 13 to 38 at depths of 22 to 38 mm, at out-of-plane distances of 1 to 15 mm, and at insertion angles of 33 to 42 degrees relative to the probe surface normal. This novel ultrasound imaging/tracking probe has strong potential to improve procedural outcomes by providing 3D needle tip locations that are co-registered to ultrasound images, while maintaining compatibility with current clinical workflow.
Influences of temperature and salinity on physicochemical properties and toxicity of zinc oxide nanoparticles to the marine diatom Thalassiosira pseudonana
Authors: Yung Mana M. N. , Kwok Kevin W. H. , Djurišić Aleksandra B. , Giesy John P. , Leung Kenneth M. Y. 
Published: June 2017

AbstractClimate change is predicted to result in rising average temperature of seawater with more extreme thermal events, and frequent rainfalls in some coastal regions. It is imperative to understand how naturally mediated changes in temperature and salinity can modulate toxicity of chemical contaminants to marine life. Thus, this study investigated combined effects of temperature and salinity on toxicity of zinc oxide nanoparticles (ZnO-NPs) to the marine diatom Thalassiosira pseudonana. Because ZnO-NPs formed larger aggregations and released less zinc ions (Zn2+) at greater temperature and salinity, toxicity of ZnO-NPs to T. pseudonana was less at 25 °C than at 10 °C and less at 32 than 12 PSU. However, toxicity of ZnO-NPs was significantly greater at 30 °C, since T. pseudonana was near its upper thermal limit. Three test compounds, ZnO, ZnO-NPs and ZnSO4, displayed different toxic potencies and resulted in different profiles of expression of genes in T. pseudonana. This indicated that ZnO-NPs caused toxicity via different pathways compared to ZnSO4. Mechanisms of toxic action of the three compounds were also dependent on temperature and salinity. These results provide insights into molecular mechanisms underlying the responses of the diatom to ZnO-NPs and Zn2+ under various regimes of temperature and salinity.
Insecticide susceptibility of Anopheles mosquitoes changes in response to variations in the larval environment
Authors: Owusu Henry F. , Chitnis Nakul , Müller Pie 
Published: June 2017

AbstractInsecticide resistance threatens the success achieved through vector control in reducing the burden of malaria. An understanding of insecticide resistance mechanisms would help to develop novel tools and strategies to restore the efficacy of insecticides. Although we have substantially improved our understanding of the genetic basis of insecticide resistance over the last decade, we still know little of how environmental variations influence the mosquito phenotype. Here, we measured how variations in larval rearing conditions change the insecticide susceptibility phenotype of adult Anopheles mosquitoes. Anopheles gambiae and A. stephensi larvae were bred under different combinations of temperature, population density and nutrition, and the emerging adults were exposed to permethrin. Mosquitoes bred under different conditions showed considerable changes in mortality rates and body weight, with nutrition being the major factor. Weight is a strong predictor of insecticide susceptibility and bigger mosquitoes are more likely to survive insecticide treatment. The changes can be substantial, such that the same mosquito colony may be considered fully susceptible or highly resistant when judged by World Health Organization discriminatory concentrations. The results shown here emphasise the importance of the environmental background in developing insecticide resistance phenotypes, and caution for the interpretation of data generated by insecticide susceptibility assays.
Impact of Module-X2 and Carbohydrate Binding Module-3 on the catalytic activity of associated glycoside hydrolases towards plant biomass
Authors: Pasari Nandita , Adlakha Nidhi , Gupta Mayank , Bashir Zeenat , Rajacharya Girish H. , Verma Garima , Munde Manoj , Bhatnagar Rakesh , Yazdani Syed Shams 
Published: June 2017

AbstractCellulolytic enzymes capable of hydrolyzing plant biomass are secreted by microbial cells specifically in response to the carbon substrate present in the environment. These enzymes consist of a catalytic domain, generally appended to one or more non-catalytic Carbohydrate Binding Module (CBM), which enhances their activity towards recalcitrant biomass. In the present study, the genome of a cellulolytic microbe Paenibacillus polymyxa A18 was annotated for the presence of CBMs and analyzed their expression in response to the plant biomass and model polysaccharides Avicel, CMC and xylan using quantitative PCR. A gene that encodes X2-CBM3 was found to be maximally induced in response to the biomass and crystalline substrate Avicel. Association of X2-CBM3 with xyloglucanase and endoglucanase led to up to 4.6-fold increase in activity towards insoluble substrates. In the substrate binding study, module X2 showed a higher affinity towards biomass and phosphoric acid swollen cellulose, whereas CBM3 showed a higher affinity towards Avicel. Further structural modeling of X2 also indicated its potential role in substrate binding. Our findings highlighted the role of module X2 along with CBM3 in assisting the enzyme catalysis of agricultural residue and paved the way to engineer glycoside hydrolases for superior activity.
XtracTB Assay, a Mycobacterium tuberculosis molecular screening test with sensitivity approaching culture
Authors: Reed Jennifer L. , Basu Debby , Butzler Matthew A. , McFall Sally M. 
Published: June 2017

AbstractNucleic acid amplification tests are increasingly used to diagnose tuberculosis (TB) due to their speed and sensitivity compared to sputum smear microscopy. However, these tests fail to equal culture’s sensitivity with sputum smear microscopy negative specimens and therefore cannot be used to rule out TB disease. For molecular tests to match culture’s sensitivity, they must detect ≤10 genomic copies of Mycobacterium tuberculosis (MTB) DNA, the limit of detection of culture, process ≥1 ml of sputum ensuring sufficient number of MTB are in the reaction, and efficiently remove sputum associated inhibitors from this large sample. Here we report the preliminary characterization of XtracTB Assay, a MTB testing protocol designed for inclusion in either an integrated point-of-care platform or a high throughput automated central laboratory system. The test combines DNA sequence specific sample prep to reduce the co-extraction of qPCR inhibitors with the amplification of two MTB specific loci (IS6110 and senX3-regX3) to increase test sensitivity and minimize the likelihood of false negatives. The analytical sensitivity of the XtracTB Assay was 5 genomic copies/ml of sputum rivaling that of culture. Furthermore, 142 valid test results yield clinical sensitivity of 94.9% (95% CI: 90.1–99.9) and specificity of 100% (95% CI: 90.0–100.0).
Diversity of endophytic mycobiota of tropical tree Tectona grandis Linn.f.: Spatiotemporal and tissue type effects
Authors: Singh Dheeraj K , Sharma Vijay K , Kumar Jitendra , Mishra Ashish , Verma Satish K , Sieber Thomas N , Kharwar Ravindra N 
Published: June 2017

AbstractFungal endophytes were isolated from leaf, bark and stem ofTectona grandisLinn.f. sampled at four geographical locations in winter, summer and monsoon seasons. The recovered 5089 isolates were assigned to 45 distinct morphotypes based on morphology. The sequences of the internal transcribed spacers (ITS) of the nrDNA of some morphotypes were identical, but morphological differences were strong enough to consider these morphotypes as separate species. Forty-three morphotypes were assigned to ascomycotina and two to basidiomycotina. Ascomycotina was the predominating group with 99.7% of total isolates followed by basidiomycotina with only 0.3% of total isolates.Diaporthe(Phomopsis) species dominated the communities independently on tissue type, location or season. More than 60% of the examined tissue pieces were colonized by members of this species complex. While these endophytes are ubiquitous others were tissue or location specific. Tissue type had the strongest effect on the species evenness of the endophytic assemblage followed by geographical location and season. However, Shannon-Wiener index (H’) significantly (p ≤ 0.001) varied with all three factors i.e. season, location and tissue type. Leaves supported the highest diversity across all the seasons and locations. In conclusion, all the three factors together determined the structure of endophytic mycobiota assemblage ofT.grandis.
Identification of transcripts with short stuORFs as targets for DENR•MCTS1-dependent translation in human cells
Authors: Schleich Sibylle , Acevedo Julieta M. , Clemm von Hohenberg Katharina , Teleman Aurelio A. 
Published: June 2017

AbstractThe non-canonical initiation factors DENR and MCTS1 have been linked to cancer and autism. We recently showed in Drosophila that DENR and MCTS1 regulate translation re-initiation on transcripts containing upstream Open Reading Frames (uORFs) with strong Kozak sequences (stuORFs). Due to the medical relevance of DENR and MCTS1, it is worthwhile identifying the transcripts in human cells that depend on DENR and MCTS1 for their translation. We show here that in humans, as in Drosophila, transcripts with short stuORFs require DENR and MCTS1 for their optimal expression. In contrast to Drosophila, however, the dependence on stuORF length in human cells is very strong, so that only transcripts with very short stuORFs coding for 1 amino acid are dependent on DENR and MCTS1. This identifies circa 100 genes as putative DENR and MCTS1 translational targets. These genes are enriched for neuronal genes and G protein-coupled receptors. The identification of DENR and MCTS1 target transcripts will serve as a basis for future studies aimed at understanding the mechanistic involvement of DENR and MCTS1 in cancer and autism.