bluuebunny/crossref_metadata_2025_split huggingface dataset:
Explosive cell lysis as a mechanism for the biogenesis of bacterial membrane vesicles and biofilms
Authors: Turnbull Lynne , Toyofuku Masanori , Hynen Amelia L. , Kurosawa Masaharu , Pessi Gabriella , Petty Nicola K. , Osvath Sarah R. , Cárcamo-Oyarce Gerardo , Gloag Erin S. , Shimoni Raz , Omasits Ulrich , Ito Satoshi , Yap Xinhui , Monahan Leigh G. , Cavaliere Rosalia , Ahrens Christian H. , Charles Ian G. , Nomura Nobuhiko , Eberl Leo , Whitchurch Cynthia B. 
Published: April 2016

AbstractMany bacteria produce extracellular and surface-associated components such as membrane vesicles (MVs), extracellular DNA and moonlighting cytosolic proteins for which the biogenesis and export pathways are not fully understood. Here we show that the explosive cell lysis of a sub-population of cells accounts for the liberation of cytosolic content in Pseudomonas aeruginosa biofilms. Super-resolution microscopy reveals that explosive cell lysis also produces shattered membrane fragments that rapidly form MVs. A prophage endolysin encoded within the R- and F-pyocin gene cluster is essential for explosive cell lysis. Endolysin-deficient mutants are defective in MV production and biofilm development, consistent with a crucial role in the biogenesis of MVs and liberation of extracellular DNA and other biofilm matrix components. Our findings reveal that explosive cell lysis, mediated through the activity of a cryptic prophage endolysin, acts as a mechanism for the production of bacterial MVs.
A vacuole-like compartment concentrates a disordered calcium phase in a key coccolithophorid alga
Authors: Sviben Sanja , Gal Assaf , Hood Matthew A. , Bertinetti Luca , Politi Yael , Bennet Mathieu , Krishnamoorthy Praveen , Schertel Andreas , Wirth Richard , Sorrentino Andrea , Pereiro Eva , Faivre Damien , Scheffel André 
Published: April 2016

AbstractCoccoliths are calcitic particles produced inside the cells of unicellular marine algae known as coccolithophores. They are abundant components of sea-floor carbonates, and the stoichiometry of calcium to other elements in fossil coccoliths is widely used to infer past environmental conditions. Here we study cryo-preserved cells of the dominant coccolithophore Emiliania huxleyi using state-of-the-art nanoscale imaging and spectroscopy. We identify a compartment, distinct from the coccolith-producing compartment, filled with high concentrations of a disordered form of calcium. Co-localized with calcium are high concentrations of phosphorus and minor concentrations of other cations. The amounts of calcium stored in this reservoir seem to be dynamic and at a certain stage the compartment is in direct contact with the coccolith-producing vesicle, suggesting an active role in coccolith formation. Our findings provide insights into calcium accumulation in this important calcifying organism.
Doublon dynamics and polar molecule production in an optical lattice
Authors: Covey Jacob P. , Moses Steven A. , Gärttner Martin , Safavi-Naini Arghavan , Miecnikowski Matthew T. , Fu Zhengkun , Schachenmayer Johannes , Julienne Paul S. , Rey Ana Maria , Jin Deborah S. , Ye Jun 
Published: April 2016

AbstractPolar molecules in an optical lattice provide a versatile platform to study quantum many-body dynamics. Here we use such a system to prepare a density distribution where lattice sites are either empty or occupied by a doublon composed of an interacting Bose-Fermi pair. By letting this out-of-equilibrium system evolve from a well-defined, but disordered, initial condition, we observe clear effects on pairing that arise from inter-species interactions, a higher partial-wave Feshbach resonance and excited Bloch-band population. These observations facilitate a detailed understanding of molecule formation in the lattice. Moreover, the interplay of tunnelling and interaction of fermions and bosons provides a controllable platform to study Bose-Fermi Hubbard dynamics. Additionally, we can probe the distribution of the atomic gases in the lattice by measuring the inelastic loss of doublons. These techniques realize tools that are generically applicable to studying the complex dynamics of atomic mixtures in optical lattices.
Scalable photonic network architecture based on motional averaging in room temperature gas
Authors: Borregaard J. , Zugenmaier M. , Petersen J. M. , Shen H. , Vasilakis G. , Jensen K. , Polzik E. S. , Sørensen A. S. 
Published: April 2016

AbstractQuantum interfaces between photons and atomic ensembles have emerged as powerful tools for quantum technologies. Efficient storage and retrieval of single photons requires long-lived collective atomic states, which is typically achieved with immobilized atoms. Thermal atomic vapours, which present a simple and scalable resource, have only been used for continuous variable processing or for discrete variable processing on short timescales where atomic motion is negligible. Here we develop a theory based on motional averaging to enable room temperature discrete variable quantum memories and coherent single-photon sources. We demonstrate the feasibility of this approach to scalable quantum memories with a proof-of-principle experiment with room temperature atoms contained in microcells with spin-protecting coating, placed inside an optical cavity. The experimental conditions correspond to a few photons per pulse and a long coherence time of the forward scattered photons is demonstrated, which is the essential feature of the motional averaging.
A new instrument to predict smoking cessation among patients with chronic obstructive pulmonary disease: an observational longitudinal study of the Trying To Quit smoking questionnaire
Authors: Lundh Lena , Alinaghizadeh Hassan , Törnkvist Lena , Gilljam Hans , Galanti Maria Rosaria 
Published: April 2016

AbstractThe Trying To Quit smoking questionnaire (TTQ), was developed to measure pressure-filled mental states, use of destructive pressure-relief strategies and ambivalent thoughts about quitting smoking among patients with COPD. The aim of this study was to evaluate whether the TTQ (available in an extended and in a reduced version) can be used to predict smoking cessation outcomes in smokers with COPD. As higher TTQ scores indicate higher degree of psychological distress, we hypothesised that TTQ scores at baseline would be negatively correlated with the probability of making a quit attempt, reducing the intensity of smoking and achieving complete abstinence during the 3 months. Smokers with COPD were recruited during planned or unplanned visits to primary healthcare centres, and 109 completed the TTQ at baseline and 85% participated in the follow-up after 3 months. Logistic regression was used to measure the association between the original (19 items) and the brief (14 item) version of TTQ scores and three outcomes: making at least one quit attempt, reducing the intensity of smoking and achieving complete abstinence. In a primary analysis among all the participants higher total score in the original version of TTQ was significantly associated with a lower probability of quit attempts. In a secondary analysis of subgroups of patients classified according to their readiness to quit, high TTQ scores at baseline were associated with lower probability of complete abstinence among patients not ready to quit (adjusted odds ratio (OR)=0.72; 95% confidence interval (CI)=0.53–0.99). Among patients ready to quit, high score on pressure-filled mental states was associated with lower probability of quit attempts (OR=0.78; 95% CI=0.66–0.94) but with higher probability of reduced smoking (OR=1.32; 95% CI=1.05–1.66). Ambivalent thoughts were associated with lower probability of all outcomes, but estimates were not statistically significant. Destructive coping strategies were inconsistently associated with the outcomes. TTQ in its original version and two of its subscales predicted smoking cessation outcomes in the anticipated direction. Therefore, this instrument may be useful in tailoring smoking cessation counselling for patients with COPD.
Pregnancy-associated serum N-glycome changes studied by high-throughput MALDI-TOF-MS
Authors: Jansen Bas C. , Bondt Albert , Reiding Karli R. , Lonardi Emanuela , de Jong Coen J. , Falck David , Kammeijer Guinevere S. M. , Dolhain Radboud J. E. M. , Rombouts Yoann , Wuhrer Manfred 
Published: April 2016

AbstractPregnancy requires partial suppression of the immune system to ensure maternal-foetal tolerance. Protein glycosylation and especially terminal sialic acid linkages, are of prime importance in regulating the pro- and anti-inflammatory immune responses. However, little is known about pregnancy-associated changes of the serum N-glycome and sialic acid linkages. Using a combination of recently developed methods, i.e. derivatisation that allows the distinction between α2,3- and α2,6-linked sialic acids by high-throughput MALDI-TOF-MS and software-assisted data processing, we analysed the serum N-glycome of a cohort of 29 healthy women at 6 time points during and after pregnancy. A total of 77 N-glycans were followed over time, confirming in part previous findings while also revealing novel associations (e.g. an increase of FA2BG1S1(6), FA2G1S1(6) and A2BG2S2(6) with delivery). From the individual glycans we calculated 42 derived traits. With these, an increase during pregnancy and decrease after delivery was observed for both α2,3- and α2,6-linked sialylation. Additionally, a difference in the recovery speed after delivery was observed for α2,3- and α2,6-linked sialylation of triantennary glycans. In conclusion, our new high-throughput workflow allowed the identification of novel plasma glycosylation changes with pregnancy.
Meiotic chromosome mobility in fission yeast is resistant to environmental stress
Authors: Illner Doris , Lorenz Alexander , Scherthan Harry 
Published: April 2016

AbstractThe formation of healthy gametes requires pairing of homologous chromosomes (homologs) as a prerequisite for their correct segregation during meiosis. Initially, homolog alignment is promoted by meiotic chromosome movements feeding into intimate homolog pairing by homologous recombination and/or synaptonemal complex formation. Meiotic chromosome movements in the fission yeast,Schizosaccharomyces pombe, depend on astral microtubule dynamics that drag the nucleus through the zygote; known as horsetail movement. The response of microtubule-led meiotic chromosome movements to environmental stresses such as ionizing irradiation (IR) and associated reactive oxygen species (ROS) is not known. Here, we show that, in contrast to budding yeast, the horsetail movement is largely radiation-resistant, which is likely mediated by a potent antioxidant defense. IR exposure of sporulatingS. pombecells induced misrepair and irreparable DNA double strand breaks causing chromosome fragmentation, missegregation and gamete death. Comparing radiation outcome in fission and budding yeast and studying meiosis with poisoned microtubules indicates that the increased gamete death after IR is innate to fission yeast. Inhibition of meiotic chromosome mobility in the face of IR failed to influence the course of DSB repair, indicating that paralysis of meiotic chromosome mobility in a genotoxic environment is not a universal response among species.
Carboxylesterase 1 Is Regulated by Hepatocyte Nuclear Factor 4α and Protects Against Alcohol- and MCD diet-induced Liver Injury
Authors: Xu Jiesi , Xu Yang , Li Yuanyuan , Jadhav Kavita , You Min , Yin Liya , Zhang Yanqiao 
Published: April 2016

AbstractThe liver is a major organ that controls hepatic and systemic homeostasis. Dysregulation of liver metabolism may cause liver injury. Previous studies have demonstrated that carboxylesterase 1 (CES1) regulates hepatic triglyceride metabolism and protects against liver steatosis. In the present study, we investigated whether CES1 played a role in the development of alcoholic liver disease (ALD) and methionine and choline-deficient (MCD) diet-induced liver injury. Both hepatocyte nuclear factor 4α (HNF4α) and CES1 were markedly reduced in patients with alcoholic steatohepatitis. Alcohol repressed both HNF4α and CES1 expression in primary hepatocytes. HNF4α regulated CES1 expression by directly binding to the proximal promoter of CES1. Global inactivation of CES1 aggravated alcohol- or MCD diet-induced liver inflammation and liver injury, likely as a result of increased production of acetaldehyde and reactive oxygen species and mitochondrial dysfunctions. Knockdown of hepatic CES1 exacerbated ethanol-induced steatohepatitis. These data indicate that CES1 plays a crucial role in protection against alcohol- or MCD diet-induced liver injury.
Facilitated receptor-recognition and enhanced bioactivity of bone morphogenetic protein-2 on magnesium-substituted hydroxyapatite surface
Authors: Huang Baolin , Yuan Yuan , Li Tong , Ding Sai , Zhang Wenjing , Gu Yuantong , Liu Changsheng 
Published: April 2016

AbstractBiomaterial surface functionalized with bone morphogenetic protein-2 (BMP-2) is a promising approach to fabricating successful orthopedic implants/scaffolds. However, the bioactivity of BMP-2 on material surfaces is still far from satisfactory and the mechanism of related protein-surface interaction remains elusive. Based on the most widely used bone-implants/scaffolds material, hydroxyapatite (HAP), we developed a matrix of magnesium-substituted HAP (Mg-HAP, 2.2 at% substitution) to address these issues. Further, we investigated the adsorption dynamics, BMPRs-recruitment, and bioactivity of recombinant human BMP-2 (rhBMP-2) on the HAP and Mg-HAP surfaces. To elucidate the mechanism, molecular dynamic simulations were performed to calculate the preferred orientations, conformation changes, and cysteine-knot stabilities of adsorbed BMP-2 molecules. The results showed that rhBMP-2 on the Mg-HAP surface exhibited greater bioactivity, evidenced by more facilitated BMPRs-recognition and higher ALP activity than on the HAP surface. Moreover, molecular simulations indicated that BMP-2 favoured distinct side-on orientations on the HAP and Mg-HAP surfaces. Intriguingly, BMP-2 on the Mg-HAP surface largely preserved the active protein structure evidenced by more stable cysteine-knots than on the HAP surface. These findings explicitly clarify the mechanism of BMP-2-HAP/Mg-HAP interactions and highlight the promising application of Mg-HAP/BMP-2 matrixes in bone regeneration implants/scaffolds.
Mechanical properties and failure behavior of unidirectional porous ceramics
Authors: Seuba Jordi , Deville Sylvain , Guizard Christian , Stevenson Adam J. 
Published: April 2016

AbstractWe show that the honeycomb out-of-plane model derived by Gibson and Ashby can be applied to describe the compressive behavior of unidirectional porous materials. Ice-templating allowed us to process samples with accurate control over pore volume, size and morphology. These samples allowed us to evaluate the effect of this microstructural variations on the compressive strength in a porosity range of 45–80%. The maximum strength of 286 MPa was achieved in the least porous ice-templated sample (P(%) = 49.9), with the smallest pore size (3 μm). We found that the out-of-plane model only holds when buckling is the dominant failure mode, as should be expected. Furthermore, we controlled total pore volume by adjusting solids loading and sintering temperature. This strategy allows us to independently control macroporosity and densification of walls and the compressive strength of ice-templated materials is exclusively dependent on total pore volume.
Persistent and energetic bottom-trapped topographic Rossby waves observed in the southern South China Sea
Authors: Shu Yeqiang , Xue Huijie , Wang Dongxiao , Chai Fei , Xie Qiang , Cai Shuqun , Chen Rongyu , Chen Ju , Li Jian , He Yunkai 
Published: April 2016

AbstractEnergetic fluctuations with periods of 9–14 days below a depth of 1400 m were observed in the southern South China Sea (SCS) from 5 years of direct measurements. We interpreted such fluctuations as topographic Rossby waves (TRWs) because they obey the dispersion relation. The TRWs persisted from May 24, 2009 to August 23, 2013, and their bottom current speed with a maximum of ~10 cm/s was one order of magnitude greater than the mean current and comparable to the tidal currents near the bottom. The bottom-trapped TRWs had an approximate trapping depth of 325 m and reference wavelength of ~82 km, which were likely excited by eddies above. Upper layer current speed that peaked approximately every 2 months could offer the energy sources for the persistent TRWs in the southern SCS. Energetic bottom-trapped TRWs may have a comparable role in deep circulation to tides in areas with complex topography.
DNA context represents transcription regulation of the gene in mouse embryonic stem cells
Authors: Ha Misook , Hong Soondo 
Published: April 2016

AbstractUnderstanding gene regulatory information in DNA remains a significant challenge in biomedical research. This study presents a computational approach to infer gene regulatory programs from primary DNA sequences. Using DNA around transcription start sites as attributes, our model predicts gene regulation in the gene. We find that H3K27ac around TSS is an informative descriptor of the transcription program in mouse embryonic stem cells. We build a computational model inferring the cell-type-specific H3K27ac signatures in the DNA around TSS. A comparison of embryonic stem cell and liver cell-specific H3K27ac signatures in DNA shows that the H3K27ac signatures in DNA around TSS efficiently distinguish the cell-type specific H3K27ac peaks and the gene regulation. The arrangement of the H3K27ac signatures inferred from the DNA represents the transcription regulation of the gene in mESC. We show that the DNA around transcription start sites is associated with the gene regulatory program by specific interaction with H3K27ac.
MgO:Li,Ce,Sm as a high-sensitivity material for Optically Stimulated Luminescence dosimetry
Authors: Oliveira Luiz C. , Yukihara Eduardo G. , Baffa Oswaldo 
Published: April 2016

AbstractThe goal of this work was to investigate the relevant dosimetric and luminescent properties of MgO:Li3%,Ce0.03%,Sm0.03%, a newly-developed, high sensitivity Optically Stimulated Luminescence (OSL) material of low effective atomic number (Zeff = 10.8) and potential interest for medical and personal dosimetry. We characterized the thermoluminescence (TL), OSL, radioluminescence (RL) and OSL emission spectrum of this new material and carried out a preliminary investigation on the OSL signal stability. MgO:Li,Ce,Sm has a main TL peak at ~180 °C (at a heating rate of 5 °C/s) associated with Ce3+ and Sm3+ emission. The results indicate that the infrared (870 nm) stimulated OSL from MgO:Li,Ce,Sm has suitable properties for dosimetry, including high sensitivity to ionizing radiation (20 times that of Al2O3:C, under the measurement conditions) and wide dynamic range (7 μGy–30 Gy). The OSL associated with Ce3+ emission is correlated with a dominant, practically isolated peak at 180 °C. Fading of ~15% was observed in the first hour, probably due to shallow traps, followed by subsequent fading of 6–7% over the next 35 days. These properties, together with the characteristically fast luminescence from Ce3+, make this material also a strong candidate for 2D OSL dose mapping.
Elevated Expression of Matrix Metalloproteinase-9 not Matrix Metalloproteinase-2 Contributes to Progression of Extracranial Arteriovenous Malformation
Authors: Wei Ting , Zhang Haihong , Cetin Neslihan , Miller Emily , Moak Teri , Suen James Y. , Richter Gresham T. 
Published: April 2016

AbstractExtracranial arteriovenous malformations (AVMs) are rare but dangerous congenital lesions arising from direct arterial-venous shunts without intervening capillaries. Progressive infiltration, expansion and soft tissue destruction lead to bleeding, pain, debilitation and disfigurement. The pathophysiology of AVMs is not well understood. Matrix Metalloproteinases (MMPs) are thought to play an important role in pathologic processes underlying many diseases. This study investigates the expression of MMP-9 and MMP-2 in aggressive extracranial AVMs. The differential expression of MMP-9 and its regulatory factors is also examined. Herein we demonstrate that mRNA and protein expressions of MMP-9, but not MMP-2, are significantly higher in AVM tissues compared to normal tissues. The serum level of MMP-9, but not MMP-2, is also elevated in AVM patients compared to healthy controls. MMP-9/neutrophil gelatinase-associated lipocalin (NGAL) complex is also significantly increased in AVM tissues. The MMP-9/ tissue inhibitor of metalloproteases-1 (TIMP-1) complex presents as a major form detected in normal tissues. The increased and aberrant expression of MMP-9 and specific MMP-9 forms may help explain the constitutive vascular remodeling and infiltrative nature of these lesions. Specific MMP-9 inhibitors would be a promising treatment for AVMs.
A pharmacological inhibitor of NLRP3 inflammasome prevents non-alcoholic fatty liver disease in a mouse model induced by high fat diet
Authors: Yang Gabsik , Lee Hye Eun , Lee Joo Young 
Published: April 2016

AbstractThe activation of NOD-like receptor family pyrin domain containing 3 (NLRP3) inflammasome is closely associated with the development and progression of non-alcoholic fatty liver disease (NAFLD) induced by a high-fat diet. Therefore, we investigated whether oral administration of sulforaphane (SFN) prevented high-fat diet-induced NAFLD in mice by regulation of the NLRP3 inflammasome in the liver. Daily oral administrations of SFN reduced hepatic steatosis scores, serum ALT and AST levels, and hepatic levels of cholesterol, triglycerides, and free fatty acids in mice fed a high-fat diet. These were correlated with the suppression of NLRP3 inflammasome activation in the liver by SFN as evidenced by decrease in mRNA levels of ASC and caspase-1, caspase-1 enzyme activity, and IL-1β levels. SFN inhibited saturated fatty acid-induced activation of the NLRP3 inflammasome in primary mouse hepatocytes, accompanied by the restoration of mitochondrial dysfunction. The suppression of NLRP3 inflammasome by SFN was mediated by the regulation of AMP-activated protein kinase-autophagy axis. Our findings demonstrated that the suppression of NLRP3 inflammasome activation by an orally available small molecule inhibitor leads to the alleviation of the hepatic steatosis symptoms associated with NAFLD induced by a high-fat diet.
First-Principle Electronic Properties of Dilute-P GaN1−xPx Alloy for Visible Light Emitters
Authors: Tan Chee-Keong , Borovac Damir , Sun Wei , Tansu Nelson 
Published: April 2016

AbstractA study on the electronic properties of the dilute-P GaN1−xPx alloy using First-Principle Density Functional Theory (DFT) calculations is presented. Our results indicate a band gap energy coverage from 3.645 eV to 2.697 eV, with P-content varying from 0% to 12.5% respectively. In addition, through line fitting of calculated and experimental data, a bowing parameter of 9.5 ± 0.5 eV was obtained. The effective masses for electrons and holes are analyzed, as well as the split-off energy parameters where findings indicate minimal interband Auger recombination. The alloy also possesses the direct energy band gap property, indicating its strong potential as a candidate for future photonic device applications.