bluuebunny/crossref_metadata_2025 huggingface dataset:
Piezoelectric enhancement under negative pressure
Authors: Kvasov Alexander , McGilly Leo J. , Wang Jin , Shi Zhiyong , Sandu Cosmin S. , Sluka Tomas , Tagantsev Alexander K. , Setter Nava
Published: July 2016

Enhancement of ferroelectric properties, both spontaneous polarization and Curie temperature under negative pressure had been predicted in the past from first principles and recently confirmed experimentally. In contrast, piezoelectric properties are expected to increase by positive pressure, through polarization rotation. Here we investigate the piezoelectric response of the classical PbTiO3, Pb(Zr,Ti)O3 and BaTiO3 perovskite ferroelectrics under negative pressure from first principles and find significant enhancement. Piezoelectric response is then tested experimentally on free-standing PbTiO3 and Pb(Zr,Ti)O3 nanowires under self-sustained negative pressure, confirming the theoretical prediction. Numerical simulations verify that negative pressure in nanowires is the origin of the enhanced electromechanical properties. The results may be useful in the development of highly performing piezoelectrics, including lead-free ones.
Hierarchical nanostructure and synergy of multimolecular signalling complexes
Authors: Sherman Eilon , Barr Valarie A. , Merrill Robert K. , Regan Carole K. , Sommers Connie L. , Samelson Lawrence E.
Published: July 2016

Signalling complexes are dynamic, multimolecular structures and sites for intracellular signal transduction. Although they play a crucial role in cellular activation, current research techniques fail to resolve their structure in intact cells. Here we present a multicolour, photoactivated localization microscopy approach for imaging multiple types of single molecules in fixed and live cells and statistical tools to determine the nanoscale organization, topology and synergy of molecular interactions in signalling complexes downstream of the T-cell antigen receptor. We observe that signalling complexes nucleated at the key adapter LAT show a hierarchical topology. The critical enzymes PLCγ1 and VAV1 localize to the centre of LAT-based complexes, and the adapter SLP-76 and actin molecules localize to the periphery. Conditional second-order statistics reveal a hierarchical network of synergic interactions between these molecules. Our results extend our understanding of the nanostructure of signalling complexes and are relevant to studying a wide range of multimolecular complexes.
Atomic-scale Studies of Uranium Oxidation and Corrosion by Water Vapour
Authors: Martin T. L. , Coe C. , Bagot P. A. J. , Morrall P. , Smith G. D. W , Scott T. , Moody M. P.
Published: July 2016

Understanding the corrosion of uranium is important for its safe, long-term storage. Uranium metal corrodes rapidly in air, but the exact mechanism remains subject to debate. Atom Probe Tomography was used to investigate the surface microstructure of metallic depleted uranium specimens following polishing and exposure to moist air. A complex, corrugated metal-oxide interface was observed, with approximately 60 at.% oxygen content within the oxide. Interestingly, a very thin (~5 nm) interfacial layer of uranium hydride was observed at the oxide-metal interface. Exposure to deuterated water vapour produced an equivalent deuteride signal at the metal-oxide interface, confirming the hydride as originating via the water vapour oxidation mechanism. Hydroxide ions were detected uniformly throughout the oxide, yet showed reduced prominence at the metal interface. These results support a proposed mechanism for the oxidation of uranium in water vapour environments where the transport of hydroxyl species and the formation of hydride are key to understanding the observed behaviour.
Correction: Corrigendum: Determining Chemically and Spatially Resolved Atomic Profile of Low Contrast Interface Structure with High Resolution
Authors: Nayak Maheswar , Pradhan P. C. , Lodha G. S. , Sokolov A. , Schäfers F.
Published: July 2016

Determining Chemically and Spatially Resolved Atomic Profile of Low Contrast Interface Structure with High Resolution
A metabolic intermediate of the fructose-asparagine utilization pathway inhibits growth of a Salmonella fraB mutant
Authors: Sabag-Daigle Anice , Blunk Henry M. , Sengupta Anindita , Wu Jikang , Bogard Alexander J. , Ali Mohamed M. , Stahl Christopher , Wysocki Vicki H. , Gopalan Venkat , Behrman Edward J. , Ahmer Brian M. M.
Published: July 2016

Insertions in the Salmonella enterica fra locus, which encodes the fructose-asparagine (F-Asn) utilization pathway, are highly attenuated in mouse models of inflammation (>1000-fold competitive index). Here, we report that F-Asn is bacteriostatic to a fraB mutant (IC50 19 μM), but not to the wild-type or a fra island deletion mutant. We hypothesized that the presence of FraD kinase and absence of FraB deglycase causes build-up of a toxic metabolite: 6-phosphofructose-aspartate (6-P-F-Asp). We used biochemical assays to assess FraB and FraD activities, and mass spectrometry to confirm that the fraB mutant accumulates 6-P-F-Asp. These results, together with our finding that mutants lacking fraD or the fra island are not attenuated in mice, suggest that the extreme attenuation of a fraB mutant stems from 6-P-F-Asp toxicity. Salmonella FraB is therefore an excellent drug target, a prospect strengthened by the absence of the fra locus in most of the gut microbiota.
Reconstructing a spatially heterogeneous epidemic: Characterising the geographic spread of 2009 A/H1N1pdm infection in England
Authors: Birrell Paul J. , Zhang Xu-Sheng , Pebody Richard G. , Gay Nigel J. , De Angelis Daniela
Published: July 2016

Understanding how the geographic distribution of and movements within a population influence the spatial spread of infections is crucial for the design of interventions to curb transmission. Existing knowledge is typically based on results from simulation studies whereas analyses of real data remain sparse. The main difficulty in quantifying the spatial pattern of disease spread is the paucity of available data together with the challenge of incorporating optimally the limited information into models of disease transmission. To address this challenge the role of routine migration on the spatial pattern of infection during the epidemic of 2009 pandemic influenza in England is investigated here through two modelling approaches: parallel-region models, where epidemics in different regions are assumed to occur in isolation with shared characteristics; and meta-region models where inter-region transmission is expressed as a function of the commuter flux between regions. Results highlight that the significantly less computationally demanding parallel-region approach is sufficiently flexible to capture the underlying dynamics. This suggests that inter-region movement is either inaccurately characterized by the available commuting data or insignificant once its initial impact on transmission has subsided.
Electrical characterization of DNA supported on nitrocellulose membranes
Authors: Ahmad Mahmoud Al , Milhem Reham M. , Panicker Neena G. , Rizvi Tahir A. , Mustafa Farah
Published: July 2016

Integrated DNA-based nanoscale electronic devices will enable the continued realization of Moore’s Law at the level of functional devices and systems. In this work, the electrical characterization of single and complementary base paired DNA has been directly measured and investigated via the use of nitrocellulose membranes. A radio frequency DAKS-3.5 was used to measure the reflection coefficients of different DNA solutions dotted onto nitrocellulose membranes. Each DNA solution was exposed to a radio frequency signal with a power of 10 dBm and with a sweep from 200 MHz up to 13.6 GHz. The conducted measurements show some distinctions between the homomeric and complementary bases due to their different electrical polarization. As revealed from the measurements conducted, with the addition of DNA oligonucleotides, the measured capacitance increased when compared with buffer medium alone. The DNA molecules could be modeled as dielectric material that can hold electrical charges. Furthermore, the complementary paired DNA molecule-based inks solutions had a higher capacitance value compared with single DNA molecules (A, C, G and T) solutions.
Competition for Cooperation: variability, benefits and heritability of relational wealth in hunter-gatherers
Authors: Chaudhary Nikhil , Salali Gul Deniz , Thompson James , Rey Aude , Gerbault Pascale , Stevenson Edward Geoffrey Jedediah , Dyble Mark , E. Page Abigail , Smith Daniel , Mace Ruth , Vinicius Lucio , Migliano Andrea Bamberg
Published: July 2016

Many defining human characteristics including theory of mind, culture and language relate to our sociality and facilitate the formation and maintenance of cooperative relationships. Therefore, deciphering the context in which our sociality evolved is invaluable in understanding what makes us unique as a species. Much work has emphasised group-level competition, such as warfare, in moulding human cooperation and sociality. However, competition and cooperation also occur within groups; and inter-individual differences in sociality have reported fitness implications in numerous non-human taxa. Here we investigate whether differential access to cooperation (relational wealth) is likely to lead to variation in fitness at the individual level among BaYaka hunter-gatherers. Using economic gift games we find that relational wealth: a) displays individual-level variation; b) provides advantages in buffering food risk and is positively associated with body mass index (BMI) and female fertility; c) is partially heritable. These results highlight that individual-level processes may have been fundamental in the extension of human cooperation beyond small units of related individuals and in shaping our sociality. Additionally, the findings offer insight in to trends related to human sociality found from research in other fields such as psychology and epidemiology.
Enhanced magneto-optical effects in composite coaxial nanowires embedded with Ag nanoparticles
Authors: Liu Qianwen , Zheng Xuanli , He Jialun , Wang Weiping , Fu Mingming , Cao Yiyan , Li Heng , Wu Yaping , Chen Ting , Zhang Chunmiao , Chen Xiaohong , Yu Binbin , Li Shuping , Kang Junyong , Wu Zhiming
Published: July 2016

Nanostructures decorated with noble metal nanoparticles (NPs) exhibit potential for use in highly sensitive optoelectronic devices through the localized surface plasmon resonance (LSPR) effect. In this study, Faraday rotation was significantly enhanced through the structural optimization of ferromagnetic (FM)/semiconductor composite nanostructures. Experimental and theoretical results revealed that the position of noble metal NPs significantly influenced the coupling of the LSPR-enhanced electromagnetic field with FM materials. Furthermore, nanostructures embedded with noble metals demonstrated an improved capability to efficiently use the electromagnetic field compared to other structures. The Faraday rotation of ZnO/Ag(NPs)/Fe was enhanced 58 fold compared to that of the ZnO(film)/Fe. This work provides a basis for the design of nanoarchitectures for miniaturized high-performance magneto-optical devices.
Marker-aided Incorporation of Xa38, a Novel Bacterial Blight Resistance Gene, in PB1121 and Comparison of its Resistance Spectrum with xa13 + Xa21
Authors: Ellur Ranjith K. , Khanna Apurva , S Gopala Krishnan. , Bhowmick Prolay K. , Vinod K. K. , Nagarajan M. , Mondal Kalyan K. , Singh Nagendra K. , Singh Kuldeep , Prabhu Kumble Vinod , Singh Ashok K.
Published: July 2016

Basmati rice is preferred internationally because of its appealing taste, mouth feel and aroma. Pusa Basmati 1121 (PB1121) is a widely grown variety known for its excellent grain and cooking quality in the international and domestic market. It contributes approximately USD 3 billion to India’s forex earning annually by being the most traded variety. However, PB1121 is highly susceptible to bacterial blight (BB) disease. A novel BB resistance geneXa38was incorporated in PB1121 from donor parent PR114-Xa38using a modified marker-assisted backcross breeding (MABB) scheme. Phenotypic selection prior to background selection was instrumental in identifying the novel recombinants with maximum recovery of recurrent parent phenome. The strategy was effective in delimiting the linkage drag to <0.5 mb upstream and <1.9 mb downstream ofXa38with recurrent parent genome recovery upto 96.9% in the developed NILs. The NILs of PB1121 carryingXa38were compared with PB1121 NILs carryingxa13 + Xa21(developed earlier in our lab) for their resistance to BB. Both NILs showed resistance against the Xoo races 1, 2, 3 and 6. Additionally,Xa38also resisted Xoo race 5 to whichxa13 + Xa21was susceptible. The PB1121 NILs carryingXa38gene will provide effective control of BB in the Basmati growing region.
Transmission enhancement based on strong interference in metal-semiconductor layered film for energy harvesting
Authors: Li Qiang , Du Kaikai , Mao Kening , Fang Xu , Zhao Ding , Ye Hui , Qiu Min
Published: July 2016

A fundamental strategy to enhance optical transmission through a continuous metallic film based on strong interference dominated by interface phase shift is developed. In a metallic film coated with a thin semiconductor film, both transmission and absorption are simultaneously enhanced as a result of dramatically reduced reflection. For a 50-nm-thick Ag film, experimental transmission enhancement factors of 4.5 and 9.5 are realized by exploiting Ag/Si non-symmetric and Si/Ag/Si symmetric geometries, respectively. These planar layered films for transmission enhancement feature ultrathin thickness, broadband and wide-angle operation, and reduced resistance. Considering one of their potential applications as transparent metal electrodes in solar cells, a calculated 182% enhancement in the total transmission efficiency relative to a single metallic film is expected. This strategy relies on no patterned nanostructures and thereby may power up a wide spectrum of energy-harvesting applications such as thin-film photovoltaics and surface photocatalysis.
Fully Mechanically Controlled Automated Electron Microscopic Tomography
Authors: Liu Jinxin , Li Hongchang , Zhang Lei , Rames Matthew , Zhang Meng , Yu Yadong , Peng Bo , Celis César Díaz , Xu April , Zou Qin , Yang Xu , Chen Xuefeng , Ren Gang
Published: July 2016

Knowledge of three-dimensional (3D) structures of each individual particles of asymmetric and flexible proteins is essential in understanding those proteins’ functions; but their structures are difficult to determine. Electron tomography (ET) provides a tool for imaging a single and unique biological object from a series of tilted angles, but it is challenging to image a single protein for three-dimensional (3D) reconstruction due to the imperfect mechanical control capability of the specimen goniometer under both a medium to high magnification (approximately 50,000–160,000×) and an optimized beam coherence condition. Here, we report a fully mechanical control method for automating ET data acquisition without using beam tilt/shift processes. This method could reduce the accumulation of beam tilt/shift that used to compensate the error from the mechanical control, but downgraded the beam coherence. Our method was developed by minimizing the error of the target object center during the tilting process through a closed-loop proportional-integral (PI) control algorithm. The validations by both negative staining (NS) and cryo-electron microscopy (cryo-EM) suggest that this method has a comparable capability to other ET methods in tracking target proteins while maintaining optimized beam coherence conditions for imaging.
Identification of novel and robust internal control genes from Volvariella volvacea that are suitable for RT-qPCR in filamentous fungi
Authors: Tao Yongxin , van Peer Arend Frans , Huang Qianhui , Shao Yanping , Zhang Lei , Xie Bin , Jiang Yuji , Zhu Jian , Xie Baogui
Published: July 2016

The selection of appropriate internal control genes (ICGs) is a crucial step in the normalization of real-time quantitative PCR (RT-qPCR) data. Housekeeping genes are habitually selected for this purpose, despite accumulating evidence on their instability. We screened for novel, robust ICGs in the mushroom forming fungus Volvariella volvacea. Nine commonly used and five newly selected ICGs were evaluated for expression stability using RT-qPCR data in eight different stages of the life cycle of V. volvacea. Three different algorithms consistently determined that three novel ICGs (SPRYp, Ras and Vps26) exhibited the highest expression stability in V. volvacea. Subsequent analysis of ICGs in twenty-four expression profiles from nine filamentous fungi revealed that Ras was the most stable ICG amongst the Basidiomycetous samples, followed by SPRYp, Vps26 and ACTB. Vps26 was expressed most stably within the analyzed data of Ascomycetes, followed by HH3 and β-TUB. No ICG was universally stable for all fungal species, or for all experimental conditions within a species. Ultimately, the choice of an ICG will depend on a specific set of experiments. This study provides novel, robust ICGs for Basidiomycetes and Ascomycetes. Together with the presented guiding principles, this enables the efficient selection of suitable ICGs for RT-qPCR.
Influence of donor–recipient sex mismatch on long-term survival of pancreatic grafts
Authors: Li Zhiwei , Mei Shengmin , Xiang Jie , Zhou Jie , Zhang Qijun , Yan Sheng , Zhou Lin , Hu Zhenhua , Zheng Shusen
Published: July 2016

To assess the role of sex mismatch on graft survival after pancreas transplantation. We evaluated 24,195 pancreas-transplant recipients reported in the Scientific Registry of Transplant Recipients over a 25-year period. Pancreatic graft survival (PGS) was analyzed according to donor–recipient sex pairing using Kaplan–Meier estimations. Hazard ratios were estimated using Cox proportional hazard models. A total of 14,187 male and 10,008 female recipients were included in final analyses. Mean follow-up was 8.3 ± 5.7 years. In multivariate analyses, neither recipient sex nor donor sex was associated with pancreatic graft failure (PGF), but donor–recipient sex mismatch (regardless of recipient sex) was an independent predictor of PGS (HR, 1.09; 95% CI, 1.04–1.14; p < 0.001). Compared with M → M sex-matched recipients in univariate analyses, M → F and F → M sex mismatches were associated with an increased risk of PGF. Adjustment for significant recipient and donor factors eliminated the association between F → M sex mismatch and PGF (HR, 1.02; 95% CI, 0.93–1.10; p = 0.752), but not M → F (1.09; 1.02–1.17; 0.020). Stratified analyses suggested that the negative effect of donor–recipient sex mismatch could be neutralized in older patients. These findings suggest that donor–recipient sex pairing should be taken into consideration in organ-allocation strategies.
Multi-functionality Redefined with Colloidal Carotene Carbon Nanoparticles for Synchronized Chemical Imaging, Enriched Cellular Uptake and Therapy
Authors: Misra Santosh K. , Mukherjee Prabuddha , Chang Huei-Huei , Tiwari Saumya , Gryka Mark , Bhargava Rohit , Pan Dipanjan
Published: July 2016

Typically, multiplexing high nanoparticle uptake, imaging and therapy requires careful integration of three different functions of a multiscale molecular-particle assembly. Here, we present a simpler approach to multiplexing by utilizing one component of the system for multiple functions. Specifically, we successfully synthesized and characterized colloidal carotene carbon nanoparticle (C3-NP), in which a single functional molecule served a threefold purpose. First, the presence of carotene moieties promoted the passage of the particle through the cell membrane and into the cells. Second, the ligand acted as a potent detrimental moiety for cancer cells and, finally, the ligands produced optical contrast for robust microscopic detection in complex cellular environments. In comparative tests, C3-NP were found to provide effective intracellular delivery that enables both robust detection at cellular and tissue level and presents significant therapeutic potential without altering the mechanism of intracellular action of β-carotene. Surface coating of C3 with phospholipid was used to generate C3-Lipocoat nanoparticles with further improved function and biocompatibility, paving the path to eventual in vivo studies.
Bursaphelenchus xylophilus is killed by homologues of 2-(1-undecyloxy)-1-ethanol
Authors: Kim Junheon , Lee Sang-Myeong , Park Chung Gyoo
Published: July 2016

2-(1-Undecyloxy)-1-ethanol, monochamol, is a male-produced aggregation pheromone of the Monochamus species, which are efficient vectors of the pine wood nematode (PWN), Bursaphelenchus xylophilus, which cause devastating damage to pines worldwide. The nematicidal activity of synthetic monochamol and its homologues (ROEtOH: R = C7-C13) were investigated to find potential alternatives to the currently used PWN control agents abamectin and emamectin. Compounds with C7-C13 chain length alkyl groups exhibited 100% nematicidal activity at a concentration of 1000 mg/L. At a concentration of 100 mg/L, 2-(1-nonyloxy)-1-ethanol (C9OEtOH), 2-(1-decyloxy)-1-ethanol (C10OEtOH), 2-(1-undecyloxy)-1-ethanol (C11OEtOH), and 2-(1-dodecyloxy)-1-ethanol (C12OEtOH) showed 100% nematicidal activity, but the others showed weaker activities. C11OEtOH showed similar nematicidal activity to abamectin in terms of LD90 values, which were 13.30 and 12.53 mg/L, respectively. However, C9OEtOH, C10OEtOH, and C12OEtOH (LC90 values: 53.63, 38.18, and 46.68 mg/L, respectively) were less effective than C11OEtOH and abamectin. These results indicate that monochamol could be an effective alternative agent against PWN. The relationship of insecticidal and nematicidal activity to different carbon chain lengths in compounds is discussed.
Single-Crystal X-ray Structures of conductive π-Stacking Dimers of Tetrakis(alkylthio)benzene Radical Cations
Authors: Chen Xiaoyu , Gao Feng , Yang Wuqin
Published: July 2016

Salts containing radical cations of 1,2,4,5-tetrakis(isopropylthio)benzene (TPB) and 1,2,4,5-tetrakis(ethylthio) benzene (TEB) have been successfully synthesized with "Equation missing". These newly synthesized salts have been characterized by UV-Vis absorption, EPR spectroscopy, conductivity measurement, single crystal X-ray diffraction analysis as well as DFT calculation. This study raises the first crystal structure of conductive π-stacking radical cation with single phenyl ring and reveals their conductivity has relationship with the stack structure which affected by the substituent.
The phase of ongoing EEG oscillations predicts the amplitude of peri-saccadic mislocalization
Authors: McLelland Douglas , Lavergne Louisa , VanRullen Rufin
Published: July 2016

Our constant eye movements mean that updating processes, such as saccadic remapping, are essential for the maintenance of a stable spatial representation of the world around us. It has been proposed that, rather than continually update a full spatiotopic map, only the location of a few key objects is updated, suggesting that the process is linked to attention. At the same time, mounting evidence links attention to oscillatory neuronal processes. We therefore hypothesized that updating processes should themselves show oscillatory characteristics, inherited from underlying attentional processes. To test this, we carried out a combined psychophysics and EEG experiment in human participants, using a saccadic mislocalization task as a behaviourally measureable proxy for spatial updating, and simultaneously recording 64-channel EEG. We then used a time-frequency analysis to test for a correlation between oscillation phase and perceptual outcome. We found a significant phase-dependence of mislocalization in a time-frequency region from around 400 ms prior to saccade initiation and peaking at around 7 Hz, principally apparent over occipital electrodes. Thus the degree of perceived mislocalization is correlated with the phase of a theta-frequency oscillation prior to saccade onset. We conclude that spatial updating processes are indeed linked to rhythmic processes in the brain.
Molecular cloning and functional characterization of the sex-determination gene doublesex in the sexually dimorphic broad-horned beetle Gnatocerus cornutus (Coleoptera, Tenebrionidae)
Authors: Gotoh Hiroki , Ishiguro Mai , Nishikawa Hideto , Morita Shinichi , Okada Kensuke , Miyatake Takahisa , Yaginuma Toshinobu , Niimi Teruyuki
Published: July 2016

Various types of weapon traits found in insect order Coleoptera are known as outstanding examples of sexually selected exaggerated characters. It is known that the sex determination genedoublesex(dsx) plays a significant role in sex-specific expression of weapon traits in various beetles belonging to the superfamily Scarabaeoidea. Although sex-specific weapon traits have evolved independently in various Coleopteran groups, developmental mechanisms of sex-specific expression have not been studied outside of the Scarabaeoidea. In order to test the hypothesis thatdsx-dependent sex-specific expression of weapon traits is a general mechanism among the Coleoptera, we have characterized thedsxin the sexually dimorphic broad-horned beetleGnatocerus cornutus(Tenebrionidea, Tenebirionidae). By using molecular cloning, we identified five splicing variants ofGnatocerus cornutus dsx(Gcdsx), which are predicted to code four different isoforms. We found one male-specific variant (GcDsx-M), two female-specific variants (GcDsx-FL and GcDsx-FS) and two non-sex-specific variants (correspond to a single isoform, GcDsx-C). Knockdown of all Dsx isoforms resulted in intersex phenotype both in male and female. Also, knockdown of all female-specific isoforms transformed females to intersex phenotype, while did not affect male phenotype. Our results clearly illustrate the important function ofGcdsxin determining sex-specific trait expression in both sexes.
Multi-scale factors influencing the characteristics of avian communities in urban parks across Beijing during the breeding season
Authors: Xie Shilin , Lu Fei , Cao Lei , Zhou Weiqi , Ouyang Zhiyun
Published: July 2016

Understanding the factors that influence the characteristics of avian communities using urban parks at both the patch and landscape level is important to focus management effort towards enhancing bird diversity. Here, we investigated this issue during the breeding season across urban parks in Beijing, China, using high-resolution satellite imagery. Fifty-two bird species were recorded across 29 parks. Analysis of residence type of birds showed that passengers were the most prevalent (37%), indicating that Beijing is a major node in the East Asian–Australasian Flyway. Park size was crucial for total species abundance, but foliage height diversity was the most important factor influencing avian species diversity. Thus, optimizing the configuration of vertical vegetation structure in certain park areas is critical for supporting avian communities in urban parks. Human visitation also showed negative impact on species diversity. At the landscape level, the percentage of artificial surface and largest patch index of woodland in the buffer region significantly affected total species richness, with insectivores and granivores being more sensitive to the landscape pattern of the buffer region. In conclusion, urban birds in Beijing are influenced by various multi-scale factors; however, these effects vary with different feeding types.
Suppression of PPARγ-mediated monoacylglycerol O-acyltransferase 1 expression ameliorates alcoholic hepatic steatosis
Authors: Yu Jung Hwan , Song Su Jin , Kim Ara , Choi Yoonjeong , Seok Jo Woon , Kim Hyo Jung , Lee Yoo Jeong , Lee Kwan Sik , Kim Jae-woo
Published: July 2016

Alcohol consumption is one of the major causes of hepatic steatosis, fibrosis, cirrhosis, and superimposed hepatocellular carcinoma. Ethanol metabolism alters the NAD+/NADH ratio, thereby suppressing the activity of sirtuin family proteins, which may affect lipid metabolism in liver cells. However, it is not clear how long-term ingestion of ethanol eventually causes lipid accumulation in liver. Here, we demonstrate that chronic ethanol ingestion activates peroxisome proliferator-activated receptor γ (PPARγ) and its target gene, monoacylglycerol O-acyltransferase 1 (MGAT1). During ethanol metabolism, a low NAD+/NADH ratio repressed NAD-dependent deacetylase sirtuin 1 (SIRT1) activity, concomitantly resulting in increased acetylated PPARγ with high transcriptional activity. Accordingly, SIRT1 transgenic mice exhibited a low level of acetylated PPARγ and were protected from hepatic steatosis driven by alcohol or PPARγ2 overexpression, suggesting that ethanol metabolism causes lipid accumulation through activation of PPARγ through acetylation. Among the genes induced by PPARγ upon alcohol consumption, MGAT1 has been shown to be involved in triglyceride synthesis. Thus, we tested the effect of MGAT1 knockdown in mice following ethanol consumption, and found a significant reduction in alcohol-induced hepatic lipid accumulation. These results suggest that MGAT1 may afford a promising approach to the treatment of fatty liver disease.
Diverse architectural properties of Sso10a proteins: Evidence for a role in chromatin compaction and organization
Authors: Driessen Rosalie P. C. , Lin Szu-Ning , Waterreus Willem-Jan , van der Meulen Alson L. H. , van der Valk Ramon A. , Laurens Niels , Moolenaar Geri F. , Pannu Navraj S. , Wuite Gijs J. L. , Goosen Nora , Dame Remus T.
Published: July 2016

Sso10a proteins are small DNA-binding proteins expressed by the crenarchaeal model organism Sulfolobus solfataricus. Based on the structure of Sso10a1, which contains a winged helix-turn-helix motif, it is believed that Sso10a proteins function as sequence-specific transcription factors. Here we show that Sso10a1 and Sso10a2 exhibit different distinct DNA-binding modes. While the ability to bend DNA is shared between the two proteins, DNA bridging is observed only for Sso10a1 and only Sso10a2 exhibits filament formation along DNA. The architectural properties of Sso10a proteins suggest that these proteins fulfil generic roles in chromatin organization and compaction. As these proteins exhibit different binding behaviour depending on their DNA binding stoichiometry, altered levels of expression in the cell can be exploited to drive changes in local genome folding, which may operate to modulate transcription.
Enhanced optoelectronic performances of vertically aligned hexagonal boron nitride nanowalls-nanocrystalline diamond heterostructures
Authors: Sankaran Kamatchi Jothiramalingam , Hoang Duc Quang , Kunuku Srinivasu , Korneychuk Svetlana , Turner Stuart , Pobedinskas Paulius , Drijkoningen Sien , Van Bael Marlies K. , D’ Haen Jan , Verbeeck Johan , Leou Keh-Chyang , Lin I-Nan , Haenen Ken
Published: July 2016

Field electron emission (FEE) properties of vertically aligned hexagonal boron nitride nanowalls (hBNNWs) grown on Si have been markedly enhanced through the use of nitrogen doped nanocrystalline diamond (nNCD) films as an interlayer. The FEE properties of hBNNWs-nNCD heterostructures show a low turn-on field of 15.2 V/μm, a high FEE current density of 1.48 mA/cm2and life-time up to a period of 248 min. These values are far superior to those for hBNNWs grown on Si substrates without the nNCD interlayer, which have a turn-on field of 46.6 V/μm with 0.21 mA/cm2FEE current density and life-time of 27 min. Cross-sectional TEM investigation reveals that the utilization of the diamond interlayer circumvented the formation of amorphous boron nitride prior to the growth of hexagonal boron nitride. Moreover, incorporation of carbon in hBNNWs improves the conductivity of hBNNWs. Such a unique combination of materials results in efficient electron transport crossing nNCD-to-hBNNWs interface and inside the hBNNWs that results in enhanced field emission of electrons. The prospective application of these materials is manifested by plasma illumination measurements with lower threshold voltage (370 V) and longer life-time, authorizing the role of hBNNWs-nNCD heterostructures in the enhancement of electron emission.
Enhanced Conversion Efficiencies in Dye-Sensitized Solar Cells Achieved through Self-Assembled Platinum(II) Metallacages
Authors: He Zuoli , Hou Zhiqiang , Xing Yonglei , Liu Xiaobin , Yin Xingtian , Que Meidan , Shao Jinyou , Que Wenxiu , Stang Peter J.
Published: July 2016

Two-component self-assembly supramolecular coordination complexes with particular photo-physical property, wherein unique donors are combined with a single metal acceptor, can be utilized for many applications including in photo-devices. In this communication, we described the synthesis and characterization of two-component self-assembly supramolecular coordination complexes (SCCs) bearing triazine and porphyrin faces with promising light-harvesting properties. These complexes were obtained from the self-assembly of a 90° Pt(II) acceptor with 2,4,6-tris(4-pyridyl)-1,3,5-triazine (TPyT) or 5,10,15,20-Tetra(4-pyridyl)-21H,23H-porphine (TPyP). The greatly improved conversion efficiencies of the dye-sensitized TiO2 solar cells were 6.79 and 6.08 respectively, while these SCCs were introduced into the TiO2 nanoparticle film photoanodes. In addition, the open circuit voltage (Voc) of dye-sensitized solar cells was also increased to 0.769 and 0.768 V, which could be ascribed to the inhibited interfacial charge recombination due to the addition of SCCs.
Capturing relativistic wakefield structures in plasmas using ultrashort high-energy electrons as a probe
Authors: Zhang C. J. , Hua J. F. , Xu X. L. , Li F. , Pai C.-H. , Wan Y. , Wu Y. P. , Gu Y. Q. , Mori W. B. , Joshi C. , Lu W.
Published: July 2016

A new method capable of capturing coherent electric field structures propagating at nearly the speed of light in plasma with a time resolution as small as a few femtoseconds is proposed. This method uses a few femtoseconds long relativistic electron bunch to probe the wake produced in a plasma by an intense laser pulse or an ultra-short relativistic charged particle beam. As the probe bunch traverses the wake, its momentum is modulated by the electric field of the wake, leading to a density variation of the probe after free-space propagation. This variation of probe density produces a snapshot of the wake that can directly give many useful information of the wake structure and its evolution. Furthermore, this snapshot allows detailed mapping of the longitudinal and transverse components of the wakefield. We develop a theoretical model for field reconstruction and verify it using 3-dimensional particle-in-cell (PIC) simulations. This model can accurately reconstruct the wakefield structure in the linear regime and it can also qualitatively map the major features of nonlinear wakes. The capturing of the injection in a nonlinear wake is demonstrated through 3D PIC simulations as an example of the application of this new method.
Endothelial cell alignment as a result of anisotropic strain and flow induced shear stress combinations
Authors: Sinha Ravi , Le Gac Séverine , Verdonschot Nico , van den Berg Albert , Koopman Bart , Rouwkema Jeroen
Published: July 2016

Endothelial cells (ECs) are continuously exposed in vivo to cyclic strain and shear stress from pulsatile blood flow. When these stimuli are applied in vitro, ECs adopt an appearance resembling their in vivo state, most apparent in their alignment (perpendicular to uniaxial strain and along the flow). Uniaxial strain and flow perpendicular to the strain, used in most in vitro studies, only represent the in vivo conditions in straight parts of vessels. The conditions present over large fractions of the vasculature can be better represented by anisotropic biaxial strains at various orientations to flow. To emulate these biological complexities in vitro, we have developed a medium-throughput device to screen for the effects on cells of variously oriented anisotropic biaxial strains and flow combinations. Upon the application of only strains for 24 h, ECs (HUVECs) aligned perpendicular to the maximum principal strain and the alignment was stronger for a higher maximum:minimum principal strain ratio. A 0.55 Pa shear stress, when applied alone or with strain for 24 h, caused cells to align along the flow. Studying EC response to such combined physiological mechanical stimuli was not possible with existing platforms and to our best knowledge, has not been reported before.
Serum metabolomics profiles in response to n-3 fatty acids in Chinese patients with type 2 diabetes: a double-blind randomised controlled trial
Authors: Zheng Ju-Sheng , Lin Mei , Imamura Fumiaki , Cai Wenwen , Wang Ling , Feng Jue-Ping , Ruan Yue , Tang Jun , Wang Fenglei , Yang Hong , Li Duo
Published: July 2016

We aimed to investigate the change of serum metabolomics in response to n-3 fatty acid supplements in Chinese patients with type 2 diabetes (T2D). In a double-blind parallel randomised controlled trial, 59 Chinese T2D patients were randomised to receive either fish oil (FO), flaxseed oil (FSO) or corn oil capsules (CO, served as a control group) and followed up for 180 days. An additional 17 healthy non-T2D participants were recruited at baseline for cross-sectional comparison between cases and non-cases. A total of 296 serum metabolites were measured among healthy controls and T2D patients before and after the intervention. Serum 3-carboxy-4-methyl-5-propyl-2-furanpropanoate (CMPF) (P-interaction = 1.8 × 10−7) was the most significant metabolite identified by repeated-measures ANOVA, followed by eicosapentaenoate (P-interaction = 4.6 × 10−6), 1-eicosapentaenoylglycerophosphocholine (P-interaction = 3.4 × 10−4), docosahexaenoate (P-interaction = 0.001), linolenate (n-3 or n-6, P-interaction = 0.005) and docosapentaenoate (n-3, P-interaction = 0.021). CMPF level was lower in T2D patients than in the healthy controls (P = 0.014) and it was significantly increased in the FO compared with CO group (P = 1.17 × 10−7). Furthermore, change of CMPF during the intervention was negatively correlated with change of serum triglycerides (P = 0.016). In conclusion, furan fatty acid metabolite CMPF was the strongest biomarker of fish oil intake. The association of CMPF with metabolic markers warrants further investigation.
Multiplex amplicon sequencing for microbe identification in community-based culture collections
Authors: Armanhi Jaderson Silveira Leite , de Souza Rafael Soares Correa , de Araújo Laura Migliorini , Okura Vagner Katsumi , Mieczkowski Piotr , Imperial Juan , Arruda Paulo
Published: July 2016

Microbiome analysis using metagenomic sequencing has revealed a vast microbial diversity associated with plants. Identifying the molecular functions associated with microbiome-plant interaction is a significant challenge concerning the development of microbiome-derived technologies applied to agriculture. An alternative to accelerate the discovery of the microbiome benefits to plants is to construct microbial culture collections concomitant with accessing microbial community structure and abundance. However, traditional methods of isolation, cultivation and identification of microbes are time-consuming and expensive. Here we describe a method for identification of microbes in culture collections constructed by picking colonies from primary platings that may contain single or multiple microorganisms, which we named community-based culture collections (CBC). A multiplexing 16S rRNA gene amplicon sequencing based on two-step PCR amplifications with tagged primers for plates, rows and columns allowed the identification of the microbial composition regardless if the well contains single or multiple microorganisms. The multiplexing system enables pooling amplicons into a single tube. The sequencing performed on the PacBio platform led to recovery near-full-length 16S rRNA gene sequences allowing accurate identification of microorganism composition in each plate well. Cross-referencing with plant microbiome structure and abundance allowed the estimation of diversity and abundance representation of microorganism in the CBC.
Analyzing the CDR3 Repertoire with respect to TCR—Beta Chain V-D-J and V-J Rearrangements in Peripheral T Cells using HTS
Authors: Ma Long , Yang Liwen , Bin Shi  , He Xiaoyan , Peng Aihua , Li Yuehong , Zhang Teng , Sun Suhong , Ma Rui , Yao Xinsheng
Published: July 2016

V-D-J rearrangement of the TCR—beta chain follows the 12/23 rule and the beyond 12/23 restriction. Currently, the proportion and characteristics of TCR—beta chain V—J rearrangement is unclear. We used high-throughput sequencing to compare and analyze TCR—beta chain V-J rearrangement and V-D-J rearrangement in the CDR3 repertoires of T cells from the PBMCs of six volunteers and six BALB/c mice. The results showed that the percentage of V-J rearrangement of the volunteers was approximately 0.7%, whereas that of the mice was 2.2%. The clonality of mice V-J rearrangement was significantly reduced compared with the V-D-J rearrangement, whereas the clonality of human V-J rearrangement was slightly reduced compared with the V-D-J rearrangement. V-J rearrangement in CDR3 involved the significant usage of N, S, F and L, whereas V-D-J rearrangement in CDR3 involved the significant usage of R and G. The levels of V deletion and J deletion in V-J rearrangement were significantly reduced compared with V-D-J rearrangement. TRBD and TRBJ usage in V-J rearrangement differed from that of V-D-J rearrangement, including dominant usage of TRBV and TRBJ and their pairing. Taken together, these results provide new ideas and technology for studies of V-D-J rearrangement and V-J rearrangement in the CDR3 repertoire.
Tempered mlo broad-spectrum resistance to barley powdery mildew in an Ethiopian landrace
Authors: Ge Xintian , Deng Weiwei , Lee Zheng Zhou , Lopez-Ruiz Francisco J. , Schweizer Patrick , Ellwood Simon R.
Published: July 2016

Recessive mutations in the Mlo gene confer broad spectrum resistance in barley (Hordeum vulgare) to powdery mildew (Blumeria graminis f. sp. hordei), a widespread and damaging disease. However, all alleles discovered to date also display deleterious pleiotropic effects, including the naturally occurring mlo-11 mutant which is widely deployed in Europe. Recessive resistance was discovered in Eth295, an Ethiopian landrace, which was developmentally controlled and quantitative without spontaneous cell wall appositions or extensive necrosis and loss of photosynthetic tissue. This resistance is determined by two copies of the mlo-11 repeat units, that occur upstream to the wild-type Mlo gene, compared to 11–12 in commonly grown cultivars and was designated mlo-11 (cnv2). mlo-11 repeat unit copy number-dependent DNA methylation corresponded with cytological and macroscopic phenotypic differences between copy number variants. Sequence data indicated mlo-11 (cnv2) formed via recombination between progenitor mlo-11 repeat units and the 3′ end of an adjacent stowaway MITE containing region. mlo-11 (cnv2) is the only example of a moderated mlo variant discovered to date and may have arisen by natural selection against the deleterious effects of the progenitor mlo-11 repeat unit configuration.
Structural and dynamics studies of a truncated variant of CI repressor from bacteriophage TP901-1
Authors: Rasmussen Kim Krighaar , Frandsen Kristian E. H. , Boeri Erba Elisabetta , Pedersen Margit , Varming Anders K. , Hammer Karin , Kilstrup Mogens , Thulstrup Peter W. , Blackledge Martin , Jensen Malene Ringkjøbing , Lo Leggio Leila
Published: July 2016

The CI repressor from the temperate bacteriophage TP901-1 consists of two folded domains, an N-terminal helix-turn-helix DNA-binding domain (NTD) and a C-terminal oligomerization domain (CTD), which we here suggest to be further divided into CTD1and CTD2. Full-length CI is a hexameric protein, whereas a truncated version, CI∆58, forms dimers. We identify the dimerization region of CI∆58 as CTD1and determine its secondary structure to be helical both within the context of CI∆58 and in isolation. To our knowledge this is the first time that a helical dimerization domain has been found in a phage repressor. We also precisely determine the length of the flexible linker connecting the NTD to the CTD. Using electrophoretic mobility shift assays and native mass spectrometry, we show that CI∆58 interacts with the OLoperator site as one dimer bound to both half-sites and with much higher affinity than the isolated NTD domain thus demonstrating cooperativity between the two DNA binding domains. Finally, using small angle X-ray scattering data and state-of-the-art ensemble selection techniques, we delineate the conformational space sampled by CI∆58 in solution and we discuss the possible role that the dynamics play in CI-repressor function.
Predictors of response to pegylated interferon in chronic hepatitis B: a real-world hospital-based analysis
Authors: Wang Yin-Chen , Yang Sien-Sing , Su Chien-Wei , Wang Yuan-Jen , Lee Kuei-Chuan , Huo Teh-Ia , Lin Han-Chieh , Huang Yi-Hsiang
Published: July 2016

Information on the efficacy of pegylated interferon (PEG-IFN) treatment of chronic hepatitis B (CHB) patients and predictors of the response based on real-world data is limited. Consecutive 201 patients who underwent PEG-IFN treatment for CHB were reviewed. A virological response (VR) was defined as a serum HBV DNA of <2000 IU/mL, and a combined response (CR) was defined a VR accompanied by serological response for hepatitis B e antigen (HBeAg)-positive CHB. For HBeAg-positive CHB patients, the HBeAg seroconversion rate and CR rate were 30.5% and 21.2% at 48 weeks after end of treatment (EOT), respectively. Baseline alanine aminotransferase (ALT) level was associated with HBeAg seroconversion, while baseline hepatitis B s antigen (HBsAg) levels of <250 IU/mL and HBV DNA <2.5 × 107 IU/mL were strongly associated with sustained off-treatment CR. For HBeAg-negative CHB, the VR rates were 85.5%, and 27.7% at EOT, and 48 weeks after EOT, respectively; a baseline HBsAg <1,250 IU/mL was associated with sustained off-treatment VR. PEG-IFN treatment has durable HBeAg seroconversion in HBeAg-positive CHB, but results in a high risk of relapse among HBeAg-negative CHB patients. Pre-treatment HBsAg level is an important predictor of VR in CHB patients undergoing PEG-IFN treatment.
Thickness Considerations of Two-Dimensional Layered Semiconductors for Transistor Applications
Authors: Zhang Youwei , Li Hui , Wang Haomin , Xie Hong , Liu Ran , Zhang Shi-Li , Qiu Zhi-Jun
Published: July 2016

Layered two-dimensional semiconductors have attracted tremendous attention owing to their demonstrated excellent transistor switching characteristics with a large ratio of on-state to off-state current, Ion/Ioff. However, the depletion-mode nature of the transistors sets a limit on the thickness of the layered semiconductor films primarily determined by a given Ion/Ioff as an acceptable specification. Identifying the optimum thickness range is of significance for material synthesis and device fabrication. Here, we systematically investigate the thickness-dependent switching behavior of transistors with a wide thickness range of multilayer-MoS2 films. A difference in Ion/Ioff by several orders of magnitude is observed when the film thickness, t, approaches a critical depletion width. The decrease in Ion/Ioff is exponential for t between 20 nm and 100 nm, by a factor of 10 for each additional 10 nm. For t larger than 100 nm, Ion/Ioff approaches unity. Simulation using technical computer-aided tools established for silicon technology faithfully reproduces the experimentally determined scaling behavior of Ion/Ioff with t. This excellent agreement confirms that multilayer-MoS2 films can be approximated as a homogeneous semiconductor with high surface conductivity that tends to deteriorate Ion/Ioff. Our findings are helpful in guiding material synthesis and designing advanced field-effect transistors based on the layered semiconductors.