bluuebunny/crossref_metadata_2025_split huggingface dataset:
Growth resumption from stationary phase reveals memory in Escherichia coli cultures
Authors: Jõers Arvi , Tenson Tanel 
Published: April 2016

AbstractFrequent changes in nutrient availability often result in repeated cycles of bacterial growth and dormancy. The timing of growth resumption can differ among isogenic cells and delayed growth resumption can lead to antibiotic tolerant persisters. Here we describe a correlation between the timing of entry into stationary phase and resuming growth in the next period of cell proliferation. E. coli cells can follow a last in first out rule: the last ones to shut down their metabolism in the beginning of stationary phase are the first to recover in response to nutrients. This memory effect can last for several days in stationary phase and is not influenced by environmental changes. We observe that the speed and heterogeneity of growth resumption depends on the carbon source. A good carbon source (glucose) can promote rapid growth resumption even at low concentrations and is seen to act more like a signal than a growth substrate. Heterogeneous growth resumption can protect the population from adverse effect of stress, investigated here using heat-shock, because the stress-resilient dormant cells are always present.
Quantifying the role of motor imagery in brain-machine interfaces
Authors: Marchesotti Silvia , Bassolino Michela , Serino Andrea , Bleuler Hannes , Blanke Olaf 
Published: April 2016

AbstractDespite technical advances in brain machine interfaces (BMI), for as-yet unknown reasons the ability to control a BMI remains limited to a subset of users. We investigate whether individual differences in BMI control based on motor imagery (MI) are related to differences in MI ability. We assessed whether differences in kinesthetic and visual MI, in the behavioral accuracy of MI and in electroencephalographic variables, were able to differentiate between high- versus low-aptitude BMI users. High-aptitude BMI users showed higher MI accuracy as captured by subjective and behavioral measurements, pointing to a prominent role of kinesthetic rather than visual imagery. Additionally, for the first time, we applied mental chronometry, a measure quantifying the degree to which imagined and executed movements share a similar temporal profile. We also identified enhanced lateralized μ-band oscillations over sensorimotor cortices during MI in high- versus low-aptitude BMI users. These findings reveal that subjective, behavioral and EEG measurements of MI are intimately linked to BMI control. We propose that poor BMI control cannot be ascribed only to intrinsic limitations of EEG recordings and that specific questionnaires and mental chronometry can be used as predictors of BMI performance (without the need to record EEG activity).
Improving the catalytic activity of isopentenyl phosphate kinase through protein coevolution analysis
Authors: Liu Ying , Yan Zhihui , Lu Xiaoyun , Xiao Dongguang , Jiang Huifeng 
Published: April 2016

AbstractProtein rational design has become more and more popular for protein engineering with the advantage of biological big-data. In this study, we described a method of rational design that is able to identify desired mutants by analyzing the coevolution of protein sequence. We employed this approach to evolve an archaeal isopentenyl phosphate kinase that can convert dimethylallyl alcohol (DMA) into precursor of isoprenoids. By designing 9 point mutations, we improved the catalytic activities of IPK about 8-foldin vitro. After introducing the optimal mutant of IPK into engineeredE. colistrain for β-carotenoids production, we found that β-carotenoids production exhibited 97% increase over the starting strain. The process of enzyme optimization presented here could be used to improve the catalytic activities of other enzymes.
Modelling of segmented high-performance thermoelectric generators with effects of thermal radiation, electrical and thermal contact resistances
Authors: Ouyang Zhongliang , Li Dawen 
Published: April 2016

AbstractIn this study, segmented thermoelectric generators (TEGs) have been simulated with various state-of-the-art TE materials spanning a wide temperature range, from 300 K up to 1000 K. The results reveal that by combining the current best p-type TE materials, BiSbTe, MgAgSb, K-doped PbTeS and SnSe with the strongest n-type TE materials, Cu-Doped BiTeSe, AgPbSbTe and SiGe to build segmented legs, TE modules could achieve efficiencies of up to 17.0% and 20.9% at ΔT = 500 K and ΔT = 700 K, respectively and a high output power densities of over 2.1 Watt cm−2 at the temperature difference of 700 K. Moreover, we demonstrate that successful segmentation requires a smooth change of compatibility factor s from one end of the TEG leg to the other, even if s values of two ends differ by more than a factor of 2. The influence of the thermal radiation, electrical and thermal contact effects have also been studied. Although considered potentially detrimental to the TEG performance, these effects, if well-regulated, do not prevent segmentation of the current best TE materials from being a prospective way to construct high performance TEGs with greatly enhanced efficiency and output power density.
A dual drug regimen synergistically blocks human parainfluenza virus infection
Authors: Bailly Benjamin , Dirr Larissa , El-Deeb Ibrahim M. , Altmeyer Ralf , Guillon Patrice , von Itzstein Mark 
Published: April 2016

AbstractHuman parainfluenza type-3 virus (hPIV-3) is one of the principal aetiological agents of acute respiratory illness in infants worldwide and also shows high disease severity in the elderly and immunocompromised, but neither therapies nor vaccines are available to treat or prevent infection, respectively. Using a multidisciplinary approach we report herein that the approved drug suramin acts as a non-competitivein vitroinhibitor of the hPIV-3 haemagglutinin-neuraminidase (HN). Furthermore, the drug inhibits viral replication in mammalian epithelial cells with an IC50of 30 μM, when applied post-adsorption. Significantly, we show in cell-based drug-combination studies using virus infection blockade assays, that suramin acts synergistically with the anti-influenza virus drug zanamivir. Our data suggests that lower concentrations of both drugs can be used to yield high levels of inhibition. Finally, using NMR spectroscopy andin silicodocking simulations we confirmed that suramin binds HN simultaneously with zanamivir. This binding event occurs most likely in the vicinity of the protein primary binding site, resulting in an enhancement of the inhibitory potential of theN-acetylneuraminic acid-based inhibitor. This study offers a potentially exciting avenue for the treatment of parainfluenza infection by a combinatorial repurposing approach of well-established approved drugs.
Reconfigurable all-dielectric metamaterial frequency selective surface based on high-permittivity ceramics
Authors: Li Liyang , Wang Jun , Wang Jiafu , Ma Hua , Du Hongliang , Zhang Jieqiu , Qu Shaobo , Xu Zhuo 
Published: April 2016

AbstractBased on effective medium theory and dielectric resonator theory, we propose the design of reconfigurable all-dielectric metamaterial frequency selective surfaces (FSSs) using high-permittivity ceramics. The FSS is composed of ceramic resonators with different band stop responses under front and side incidences. By mechanically tuning the orientation of the ceramic resonators, reconfigurable electromagnetic (EM) responses between two adjacent stopbands can be achieved. The two broad stopbands originate from the first two resonant modes of the ceramic resonators. As an example, a reconfigurable FSS composed of cross-shaped ceramic resonators is demonstrated. Both numerical and experimental results show that the FSS can switch between two consecutive stopbands in 3.55–4.60 GHz and 4.54–4.94 GHz. The design method can be readily extended to the design of FSSs in other frequencies for high-power applications.
Procaspase-9 induces its cleavage by transnitrosylating XIAP via the Thioredoxin system during cerebral ischemia-reperfusion in rats
Authors: Zhang Dengyue , Zhao Ningjun , Ma Bin , Wang Yan , Zhang Gongliang , Yan Xianliang , Hu Shuqun , Xu Tie 
Published: April 2016

AbstractTransnitrosylation is an important mechanism by which nitric oxide (NO) modulates cell signaling pathways. For instance, SNO-caspase-3 can transnitrosylate the X-linked inhibitor of apoptosis (XIAP) to enhance apoptosis. XIAP is a potent antagonist of caspase apoptotic activity. Decrease in XIAP activity via nitrosylation results in SNO-XIAP-mediated caspase activation. Considering the functional liaison of procaspase-9 and XIAP, we hypothesized that procaspase-9 nitrosylates XIAP directly. Our data confirmed that cerebral ischemia-reperfusion induced XIAP nitrosylation, procaspase-9 denitrosylation and cleavage. Interestingly, the time courses of the nitrosylation of procaspase-9 and XIAP were negatively correlated, which was more prominent after cerebral ischemia-reperfusion, suggesting a direct interaction. The nitrosylation of XIAP, as well as the denitrosylation and cleavage of procaspase-9, were inhibited by DNCB, TrxR1 AS-ODNs, or TAT-AVPY treatment. Meanwhile, DNCB, TrxR1 AS-ODNs, or TAT-AVPY also inhibited the decrease in hippocampal CA1 neurons induced by ischemia-reperfusion in rats. The denitrosylation and cleavage of procaspase-9 induced by OGD/reoxygenation in SH-SY5Y cells were inhibited when cells were co-transfected with wild-type procaspase-9 and XIAP mutant (C449G). These data suggest that cerebral ischemia-reperfusion induces a transnitrosylation from procaspase-9 to XIAP via the Trx system to consequently cause apoptosis. Additionally, Cys325 is a critical S-nitrosylation site of procaspase-9.
Chromatin architecture may dictate the target site for DMC1, but not for RAD51, during homologous pairing
Authors: Kobayashi Wataru , Takaku Motoki , Machida Shinichi , Tachiwana Hiroaki , Maehara Kazumitsu , Ohkawa Yasuyuki , Kurumizaka Hitoshi 
Published: April 2016

AbstractIn eukaryotes, genomic DNA is compacted as chromatin, in which histones and DNA form the nucleosome as the basic unit. DMC1 and RAD51 are essential eukaryotic recombinases that mediate homologous chromosome pairing during homologous recombination. However, the means by which these two recombinases distinctly function in chromatin have remained elusive. Here we found that, in chromatin, the human DMC1-single-stranded DNA complex bypasses binding to the nucleosome, and preferentially promotes homologous pairing at the nucleosome-depleted regions. Consistently, DMC1 forms ternary complex recombination intermediates with the nucleosome-free DNA or the nucleosome-depleted DNA region. Surprisingly, removal of the histone tails improperly enhances the nucleosome binding by DMC1. In contrast, RAD51 does not specifically target the nucleosome-depleted region in chromatin. These are the first demonstrations that the chromatin architecture specifies the sites to promote the homologous recombination reaction by DMC1, but not by RAD51.
Structural properties of Sb2S3 under pressure: evidence of an electronic topological transition
Authors: Efthimiopoulos Ilias , Buchan Cienna , Wang Yuejian 
Published: April 2016

AbstractHigh-pressure Raman spectroscopy and x-ray diffraction of Sb2S3 up to 53 GPa reveals two phase transitions at 5 GPa and 15 GPa. The first transition is evidenced by noticeable compressibility changes in distinct Raman-active modes, in the lattice parameter axial ratios, the unit cell volume, as well as in specific interatomic bond lengths and bond angles. By taking into account relevant results from the literature, we assign these effects to a second-order isostructural transition arising from an electronic topological transition in Sb2S3 near 5 GPa. Close comparison between Sb2S3 and Sb2Se3 up to 10 GPa reveals a slightly diverse structural behavior for these two compounds after the isostructural transition pressure. This structural diversity appears to account for the different pressure-induced electronic behavior of Sb2S3 and Sb2Se3 up to 10 GPa, i.e. the absence of an insulator-metal transition in Sb2S3 up to that pressure. Finally, the second high-pressure modification appearing above 15 GPa appears to trigger a structural disorder at ~20 GPa; full decompression from 53 GPa leads to the recovery of an amorphous state.
Deficiency of the TLR4 analogue RP105 aggravates vein graft disease by inducing a pro-inflammatory response
Authors: Wezel Anouk , de Vries Margreet R. , Maassen Johanna M. , Kip Peter , Peters Erna A. , Karper Jacco C. , Kuiper Johan , Bot Ilze , Quax Paul H. A. 
Published: April 2016

AbstractVenous grafts are often used to bypass occlusive atherosclerotic lesions; however, poor patency leads to vein graft disease. Deficiency of TLR4, an inflammatory regulator, reduces vein graft disease. Here, we investigate the effects of the accessory molecule and TLR4 analogue RadioProtective 105 (RP105) on vein graft disease. RP105 deficiency resulted in a 90% increase in vein graft lesion area compared to controls. In a hypercholesterolemic setting (LDLr−/−/RP105−/− versus LDLr−/− mice), which is of importance as vein graft disease is usually characterized by excessive atherosclerosis, total lesion area was not affected. However we did observe an increased number of unstable lesions and intraplaque hemorrhage upon RP105 deficiency. In both setups, lesional macrophage content and lesional CCL2 was increased. In vitro, RP105−/− smooth muscle cells and mast cells secreted higher levels of CCL2. In conclusion, aggravated vein graft disease caused by RP105 deficiency results from an increased local inflammatory response.
Alteration of podocyte phenotype in the urine of women with preeclampsia
Authors: Zhai Tianyue , Furuta Itsuko , Akaishi Rina , Ishikawa Satoshi , Morikawa Mamoru , Yamada Takahiro , Koyama Takahiro , Minakami Hisanori 
Published: April 2016

AbstractPodocyte injury has been suggested to induce phenotypic alteration of glomerular podocytes and accelerate the detachment of podocytes from the glomeruli resulting in podocyturia. However, it is not clear whether podocyte phenotypic alteration occurs in the urine of women with preeclampsia (PE). Seventy-seven and 116 pelleted urine samples from 38 and 18 women at various stages of normal and PE pregnancies, respectively underwent quantitative analysis of podocyte-specific or associated protein mRNA expression, including podocin, nephrin, and synaptopodin using RT-PCR. Significant proteinuria in pregnancy (SPIP) is defined as protein:creatinine ratio (P/Cr, mg/mg) ≥0.27 in the urine supernatant. All three urine-pellet mRNAs expression levels were significantly positively correlated with P/Cr levels, suggesting that podocyturia increased with proteinuria. The podocin:nephrin mRNA ratio (PNR) and synaptopodin:nephrin mRNA ratio (SNR) increased significantly with increasing P/Cr, while the podocin:synaptopodin mRNA ratio (PSR) did not change significantly according to P/Cr, resulting in significantly higher PNR and SNR, but not PSR levels, in urine from PE women with than without SPIP. The PNR, SNR, and PSR in urine from PE women before onset of SPIP were comparable to those from controls. Thus, nephrin mRNA expression was reduced in the podocytes recovered from PE women.
Unexpected Temperature Behavior of Polyethylene Glycol Spacers in Copolymer Dendrimers in Chloroform
Authors: Markelov Denis A. , Matveev Vladimir V. , Ingman Petri , Nikolaeva Marianna N. , Penkova Anastasia V. , Lahderanta Erkki , Boiko Natalia I. , Chizhik Vladimir I. 
Published: April 2016

AbstractWe have studied copolymer dendrimer structure: carbosilane dendrimers with terminal phenylbenzoate mesogenic groups attached by poly(ethylene) glycol (PEG) spacers. In this system PEG spacers are additional tuning to usual copolymer structure: dendrimer with terminal mesogenic groups. The dendrimer macromolecules were investigated in a dilute chloroform solution by 1H NMR methods (spectra and relaxations). It was found that the PEG layer in G = 5 generations dendrimer is “frozen” at high temperatures (above 260 K), but it unexpectedly becomes “unfrozen” at temperatures below 250 K (i.e., melting when cooling). The transition between these two states occurs within a small temperature range (~10 K). Such a behavior is not observed for smaller dendrimer generations (G = 1 and 3). This effect is likely related to the low critical solution temperature (LCST) of PEG and is caused by dendrimer conformations, in which the PEG group concentration in the layer increases with growing G. We suppose that the unusual behavior of PEG fragments in dendrimers will be interesting for practical applications such as nanocontainers or nanoreactors.
Tracking brain arousal fluctuations with fMRI
Authors: Chang Catie , Leopold David A. , Schölvinck Marieke Louise , Mandelkow Hendrik , Picchioni Dante , Liu Xiao , Ye Frank Q. , Turchi Janita N. , Duyn Jeff H. 
Published: April 2016

Significance
Changes in vigilance and arousal levels can interfere with the study of brain function with functional MRI (fMRI). However, the difficulty of tracking and modeling arousal state during fMRI typically precludes the assessment of arousal-dependent influences on fMRI measurements. Here, we present evidence that continuous variations in arousal level may be monitored from fMRI data alone and validate this approach with a combination of fMRI, intracortical electrophysiology, and a behavioral measure of arousal. We describe a spatial pattern whose time-varying expression in the fMRI data is found to track both electrophysiological and behavioral arousal fluctuations. These findings have implications for increasing the sensitivity of fMRI as a cognitive and clinical biomarker.
Bulk storage of “Wonderful” pomegranate fruit using modified atmosphere bags
Authors: Porat Ron , Kosto Itzhak , Daus Avinoam 
Published: April 2016

“Wonderful” pomegranates can be stored under modified atmosphere (MA) conditions for up to 3–4 months after harvest. Until recently, the harvested fruit first needed to be transferred to the packing house and packed in MA bags in cartons or plastic boxes before cooling to the desired temperature and subsequent cold storage. During the last few years, together with StePac Ltd, we have developed a new methodology in which “Wonderful” pomegranate fruit are directly harvested into large 80 kg or even 320 kg bulkXtend® MA bags in harvest bins, and then immediately transferred from the field to commercial cold storage rooms without the necessity of repacking the fruit at the packing house. In this study, we evaluated the postharvest storage performance and fruit quality of “Wonderful” pomegranates stored in bulk 80 kgXtend® MA bags in harvest bins for various periods of 4, 8, 12, and 16 weeks at 7 °C followed by 1 week in shelf life conditions at 20 °C. The results show that “Wonderful” pomegranates can be maintained in bulkXtend® MA bags in harvest bins at excellent quality with minimal losses for at least 12 weeks after harvest. Overall, this new suggested procedure allows direct transfer of large volumes of fruit from the field to cold storage rooms without intermediate transferring to the packing house, thus saving precious time and extra packaging and labor costs, and ensuring better maintenance of the cold storage chain.
A novel non-thermostable deuterolysin from Aspergillus oryzae
Authors: Maeda Hiroshi , Katase Toru , Sakai Daisuke , Takeuchi Michio , Kusumoto Ken-Ichi , Amano Hitoshi , Ishida Hiroki , Abe Keietsu , Yamagata Youhei 
Published: April 2016

Abstract
Three putative deuterolysin (EC 3.4.24.29) genes (deuA, deuB, and deuC) were found in the Aspergillus oryzae genome database (http://www.bio.nite.go.jp/dogan/project/view/AO). One of these genes, deuA, was corresponding to NpII gene, previously reported. DeuA and DeuB were overexpressed by recombinant A. oryzae and were purified. The degradation profiles against protein substrates of both enzymes were similar, but DeuB showed wider substrate specificity against peptidyl MCA-substrates compared with DeuA. Enzymatic profiles of DeuB except for thermostability also resembled those of DeuA. DeuB was inactivated by heat treatment above 80° C, different from thermostable DeuA. Transcription analysis in wild type A. oryzae showed only deuB was expressed in liquid culture, and the addition of the proteinous substrate upregulated the transcription. Furthermore, the NaNO3 addition seems to eliminate the effect of proteinous substrate for the transcription of deuB.
FlashPCA: fast sparse canonical correlation analysis of genomic data
Authors: Abraham Gad , Inouye Michael 
Published: April 2016

SummarySparse canonical correlation analysis (SCCA) is a useful approach for correlating one set of measurements, such as single nucleotide polymorphisms (SNPs), with another set of measurements, such as gene expression levels. We present a fast implementation of SCCA, enabling rapid analysis of hundreds of thousands of SNPs together with thousands of phenotypes. Our approach is implemented both as an R package flashpcaR and within the standalone commandline tool flashpca.Availability and implementationhttps://github.com/gabraham/flashpcaContactgad.abraham@unimelb.edu.au
Environmental responses, not species interactions, determine synchrony of dominant species in semiarid grasslands
Authors: Tredennick Andrew T. , de Mazancourt Claire , Loreau Michel , Adler Peter B. 
Published: April 2016

AbstractTemporal asynchrony among species helps diversity to stabilize ecosystem functioning, but identifying the mechanisms that determine synchrony remains a challenge. Here, we refine and test theory showing that synchrony depends on three factors: species responses to environmental variation, interspecific interactions, and demographic stochasticity. We then conduct simulation experiments with empirical population models to quantify the relative influence of these factors on the synchrony of dominant species in five semiarid grasslands. We found that the average synchrony of per capita growth rates, which can range from 0 (perfect asynchrony) to 1 (perfect synchrony), was higher when environmental variation was present (0.62) rather than absent (0.43). Removing interspecific interactions and demographic stochasticity had small effects on synchrony. For the dominant species in these plant communities, where species interactions and demographic stochasticity have little influence, synchrony reflects the covariance in species responses to the environment.