bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcriptional timing and noise of yeast cell cycle regulators—a single cell and single molecule approach
Authors: Amoussouvi Aouefa , Teufel Lotte , Reis Matthias , Seeger Martin , Schlichting Julia Katharina , Schreiber Gabriele , Herrmann Andreas , Klipp Edda
Published: May 2018

Gene expression is a stochastic process and its appropriate regulation is critical for cell cycle progression. Cellular stress response necessitates expression reprogramming and cell cycle arrest. While previous studies are mostly based on bulk experiments influenced by synchronization effects or lack temporal distribution, time-resolved methods on single cells are needed to understand eukaryotic cell cycle in context of noisy gene expression and external perturbations. Using smFISH, microscopy and morphological markers, we monitored mRNA abundances over cell cycle phases and calculated transcriptional noise for SIC1, CLN2, and CLB5, the main G1/S transition regulators in budding yeast. We employed mathematical modeling for in silico synchronization and for derivation of time-courses from single cell data. This approach disclosed detailed quantitative insights into transcriptional regulation with and without stress, not available from bulk experiments before. First, besides the main peak in G1 we found an upshift of CLN2 and CLB5 expression in late mitosis. Second, all three genes showed basal expression throughout cell cycle enlightening that transcription is not divided in on and off but rather in high and low phases. Finally, exposing cells to osmotic stress revealed different periods of transcriptional inhibition for CLN2 and CLB5 and the impact of stress on cell cycle phase duration. Combining experimental and computational approaches allowed us to precisely assess cell cycle progression timing, as well as gene expression dynamics.
Thomson scattering in inhomogeneous plasmas: The Role of the Fluctuation-Dissipation Theorem
Authors: Belyi V. V.
Published: May 2018

A self-consistent kinetic theory of Thomson scattering of an electromagnetic field by a non-uniform plasma is derived. We draw the readers’ attention to the inconsistency in recent results on the Thomson scattering in inhomogeneous plasma, which leads to violation of the Fluctuation-Dissipation Theorem. We show, that not only the imaginary part, but also the derivatives of the real part of the dielectric susceptibility determine the amplitude and the width of the Thomson scattering spectral lines. As a result of inhomogeneity, these properties become asymmetric with respect to inversion of the sign of the frequency. A method is proposed for measuring local gradients of the electron density with the aid of Thomson scattering.

Arising from: P. Kozlowski, et al. Sci. Rep. 6, 24283 (2016); https://doi.org/10.1038/srep24283.
An Oil-Free Picodrop Bioassay Platform for Synthetic Biology
Authors: Siltanen Christian A. , Cole Russell H. , Poust Sean , Chao Lawrence , Tyerman Jabus , Kaufmann-Malaga Benjamin , Ubersax Jeff , Gartner Zev J. , Abate Adam R.
Published: May 2018

Droplet microfluidics enables massively-parallel analysis of single cells, biomolecules, and chemicals, making it valuable for high-throughput screens. However, many hydrophobic analytes are soluble in carrier oils, preventing their quantitative analysis with the method. We apply Printed Droplet Microfluidics to construct defined reactions with chemicals and cells incubated under air on an open array. The method interfaces with most bioanalytical tools and retains hydrophobic compounds in compartmentalized reactors, allowing their quantitation.
Trophic overlap between expanding and contracting fish predators in a range margin undergoing change
Authors: Westerbom Mats , Lappalainen Antti , Mustonen Olli , Norkko Alf
Published: May 2018

Climate change is predicted to cause a freshening of the Baltic Sea, facilitating range expansions of freshwater species and contractions of marine. Resident marine flounders (Platichthys flesus) and expansive freshwater roach (Rutilus rutilus) are dominant consumers in the Baltic Sea sublittoral where they occur in partial sympatry. By comparing patterns of resource use by flounders and roach along a declining resource gradient of blue mussels (Mytilus trossulus) our aim was to explore predator functional responses and the degree of trophic overlap. Understanding the nature of density-dependent prey acquisition has important implications for predicting population dynamics of both predators and their shared prey. Results showed a highly specialized diet for both species, high reliance on blue mussels throughout the range, similar prey size preference and high trophic overlap. Highest overlap occurred where blue mussels were abundant but overlap was also high where they were scarce. Our results highlight the importance of a single food item - the blue mussel - for both species, likely promoting high population size and range expansion of roach. Findings also suggest that range expansion of roach may have a top-down structuring force on mussels that differ in severity and location from that originating from resident flounders.
Correlating the nanostructure of Al-oxide with deposition conditions and dielectric contributions of two-level systems in perspective of superconducting quantum circuits
Authors: Fritz S. , Seiler A. , Radtke L. , Schneider R. , Weides M. , Weiß G. , Gerthsen D.
Published: May 2018

This work is concerned with Al/Al-oxide(AlOx)/Al-layer systems which are important for Josephson-junction-based superconducting devices such as quantum bits. The device performance is limited by noise, which has been to a large degree assigned to the presence and properties of two-level tunneling systems in the amorphous AlOx tunnel barrier. The study is focused on the correlation of the fabrication conditions, nanostructural and nanochemical properties and the occurrence of two-level tunneling systems with particular emphasis on the AlOx-layer. Electron-beam evaporation with two different processes and sputter deposition were used for structure fabrication, and the effect of illumination by ultraviolet light during Al-oxide formation is elucidated. Characterization was performed by analytical transmission electron microscopy and low-temperature dielectric measurements. We show that the fabrication conditions have a strong impact on the nanostructural and nanochemical properties of the layer systems and the properties of two-level tunneling systems. Based on the understanding of the observed structural characteristics, routes are suggested towards the fabrication of Al/AlOx/Al-layers systems with improved properties.
Assessing the utility of frequency tagging for tracking memory-based reactivation of word representations
Authors: Lewis Ashley Glen , Schriefers Herbert , Bastiaansen Marcel , Schoffelen Jan-Mathijs
Published: May 2018

Reinstatement of memory-related neural activity measured with high temporal precision potentially provides a useful index for real-time monitoring of the timing of activation of memory content during cognitive processing. The utility of such an index extends to any situation where one is interested in the (relative) timing of activation of different sources of information in memory, a paradigm case of which is tracking lexical activation during language processing. Essential for this approach is that memory reinstatement effects are robust, so that their absence (in the average) definitively indicates that no lexical activation is present. We used electroencephalography to test the robustness of a reported subsequent memory finding involving reinstatement of frequency-specific entrained oscillatory brain activity during subsequent recognition. Participants learned lists of words presented on a background flickering at either 6 or 15 Hz to entrain a steady-state brain response. Target words subsequently presented on a non-flickering background that were correctly identified as previously seen exhibited reinstatement effects at both entrainment frequencies. Reliability of these statistical inferences was however critically dependent on the approach used for multiple comparisons correction. We conclude that effects are not robust enough to be used as a reliable index of lexical activation during language processing.
Massively Parallel Coincidence Counting of High-Dimensional Entangled States
Authors: Reichert Matthew , Defienne Hugo , Fleischer Jason W.
Published: May 2018

Entangled states of light are essential for quantum technologies and fundamental tests of physics. Current systems rely on entanglement in 2D degrees of freedom, e.g., polarization states. Increasing the dimensionality provides exponential speed-up of quantum computation, enhances the channel capacity and security of quantum communication protocols, and enables quantum imaging; unfortunately, characterizing high-dimensional entanglement of even bipartite quantum states remains prohibitively time-consuming. Here, we develop and experimentally demonstrate a new theory of camera detection that leverages the massive parallelization inherent in an array of pixels. We show that a megapixel array, for example, can measure a joint Hilbert space of 1012 dimensions, with a speed-up of nearly four orders-of-magnitude over traditional methods. The technique uses standard geometry with existing technology, thus removing barriers of entry to quantum imaging experiments, generalizes readily to arbitrary numbers of entangled photons, and opens previously inaccessible regimes of high-dimensional quantum optics.
Genome-wide analysis of circular RNAs in bovine cumulus cells treated with BMP15 and GDF9
Authors: Fu Yao , Jiang Hao , Liu Jian-Bo , Sun Xu-Lei , Zhang Zhe , Li Sheng , Gao Yan , Yuan Bao , Zhang Jia-Bao
Published: May 2018

Circular RNAs (circRNAs) are important members of the non-coding RNA family, and those relating to animal physiologies have been widely studied in recent years. This study aimed to explore the roles of circRNAs in the regulation of follicular development. We constructed four bovine cumulus cell cDNA libraries, including a negative control group (NC) and groups treated with BMP15, GDF9 and BMP15 + GDF9, and we sequenced the libraries on the Illumina HiSeq Xten platform. We identified 1706 circRNAs and screened for differential circRNA expression. We conducted a bioinformatics analysis of these circRNAs and screened for differential circRNAs. Functional annotation and enrichment analysis of the host genes showed that the differential circRNAs were related to locomotion, reproduction, biological adhesion, growth, rhythmic processes, biological phases and hormone secretion. According to the differential expression of circRNA between groups, there were 3 up-regulated and 6 down-regulated circRNAs in the BMP15 group as well as 12 up-regulated and 24 down-regulated circRNAs in the GDF9 group. Co-addition of both BMP15 and GDF9 resulted in 15 up-regulated and 13 down-regulated circRNAs. circ_n/a_75,circ_12691_1 and circ_n/a_303 were altered in both the BMP15 and GDF9 groups as well as in the BMP15 + GDF9 combination group. We focused on these three circRNAs because they were potentially associated with the additive effect of BMP15 and GDF9. Quantitative PCR analysis showed that the expression levels of these three circRNAs were consistent with the sequencing results. In addition, the target miRNAs of circ_n/a_75 and circ_n/a_303, miR-339a, miR-2400 and miR-30c, were down-regulated in the experimental group, which was in contrast to the circRNAs trend. These findings demonstrated that BMP15 and GDF9 may regulate the target gene through circRNA, as a miRNA sponge, in order to regulate the status of bovine cumulus cells and affect follicular development.
Spin supersolid phase in coupled alternating spin chains
Authors: Heydarinasab F. , Abouie J.
Published: May 2018

We study the ground state phase diagram of a two dimensional mixed-spin system of coupled alternating spin-1 and 1/2 chains with a stripe supersolid phase. Utilizing different analytical and numerical approaches such as mean field approximation, cluster mean field theory and linear spin wave theory, we demonstrate that our system displays a rich ground state phase diagram including novel stripe supersolid, solids with different fillings and super-counterfluid phases, in addition to a stripe solid with half filling, superfluid and Mott insulating phases. In order to find a minimal mixed-spin model for stripe supersolidity, in the second part of the paper we consider two kinds of mixed-spin system of coupled alternating spin-1 and 1/2 chains with (i) anisotropic nearest neighbor interactions, (ii) anisotropic hoppings and study their ground state phase diagrams. We demonstrate that, for the systems with uniform hoppings, the repulsive intra-chains interactions are necessary for stripe supersolidity. In this case the minimal two dimensional mixed-spin model is a system of spin-1 and spin-1/2 XXZ chains, interacting via Ising Hamiltonian. In the case of anisotropic hoppings, a system of coupled Ising chains is the minimal model.
Archetypal transcriptional blocks underpin yeast gene regulation in response to changes in growth conditions
Authors: Talavera David , Kershaw Christopher J. , Costello Joseph L. , Castelli Lydia M. , Rowe William , Sims Paul F. G. , Ashe Mark P. , Grant Chris M. , Pavitt Graham D. , Hubbard Simon J.
Published: May 2018

The transcriptional responses of yeast cells to diverse stresses typically include gene activation and repression. Specific stress defense, citric acid cycle and oxidative phosphorylation genes are activated, whereas protein synthesis genes are coordinately repressed. This view was achieved from comparative transcriptomic experiments delineating sets of genes whose expression greatly changed with specific stresses. Less attention has been paid to the biological significance of 1) consistent, albeit modest, changes in RNA levels across multiple conditions, and 2) the global gene expression correlations observed when comparing numerous genome-wide studies. To address this, we performed a meta-analysis of 1379 microarray-based experiments in yeast, and identified 1388 blocks of RNAs whose expression changes correlate across multiple and diverse conditions. Many of these blocks represent sets of functionally-related RNAs that act in a coordinated fashion under normal and stress conditions, and map to global cell defense and growth responses. Subsequently, we used the blocks to analyze novel RNA-seq experiments, demonstrating their utility and confirming the conclusions drawn from the meta-analysis. Our results provide a new framework for understanding the biological significance of changes in gene expression: ‘archetypal’ transcriptional blocks that are regulated in a concerted fashion in response to external stimuli.
The Cardiometabolic Burden of Self-Perceived Obesity: A Multilevel Analysis of a Nationally Representative Sample of Korean Adults
Authors: Kim Yongjoo , Austin S. Bryn , Subramanian S V , Kawachi Ichiro
Published: May 2018

Emerging evidence has shown that self-perception of overweight/obese status is associated with unfavorable cardiometabolic outcomes, above and beyond actual body weight. Given the lack of research among Asian populations, we examined the association between weight perception and metabolic syndrome (MetS) and cardiometabolic risks among Koreans. Data from the 2010–2015 Korea National Health and Nutrition Examination Survey, including women (N = 12,181) and men (N = 9,448) aged 19–65 years, were analyzed. Weight status perception was measured by participants’ self-evaluation of their body size (“very/slightly obese,” “normal,” and “very/slightly thin”). Overall, 23.2% of women and 28.7% of men had MetS. Our cross-sectional multilevel logistic analyses showed a significant positive association between self-perceived obesity (vs. perceived normal weight) and MetS, independent of BMI and sociodemographic/behavioral/medical conditions, with a stronger association detected among men (OR = 1.38, p < 0.05) than women (OR = 1.22, p < 0.05), confirmed by a statistically significant interaction. Additionally, perceived obesity was associated with high blood pressure (OR = 1.27, p < 0.05) and high triglycerides (OR = 1.38, p < 0.05) among men and low high-density lipoprotein cholesterol (OR = 1.15, p < 0.05) among women. While further prospective research is needed, our findings suggest that perception of being obese may be an unfavorable indicator of cardiometabolic health among Koreans regardless of actual body weight.
North American domestic pigs are susceptible to experimental infection with Japanese encephalitis virus
Authors: Park So Lee , Huang Yan-Jang S. , Lyons Amy C. , Ayers Victoria B. , Hettenbach Susan M. , McVey D. Scott , Burton Kenneth R. , Higgs Stephen , Vanlandingham Dana L.
Published: May 2018

Japanese encephalitis virus (JEV) is a mosquito-borne flavivirus that is capable of causing encephalitic diseases in children. While humans can succumb to severe disease, the transmission cycle is maintained by viremic birds and pigs in endemic regions. Although JEV is regarded as a significant threat to the United States (U.S.), the susceptibility of domestic swine to JEV infection has not been evaluated. In this study, domestic pigs from North America were intravenously challenged with JEV to characterize the pathological outcomes. Systemic infection followed by the development of neutralizing antibodies were observed in all challenged animals. While most clinical signs were limited to nonspecific symptoms, virus dissemination and neuroinvasion was observed at the acute phase of infection. Detection of infectious viruses in nasal secretions suggest infected animals are likely to promote the vector-free transmission of JEV. Viral RNA present in tonsils at 28 days post infection demonstrates the likelihood of persistent infection. In summary, our findings indicate that domestic pigs can potentially become amplification hosts in the event of an introduction of JEV into the U.S. Vector-free transmission to immunologically naïve vertebrate hosts is also likely through nasal shedding of infectious viruses.
Thermodynamic and crystallographic model for anion uptake by hydrated calcium aluminate (AFm): an example of molybdenum
Authors: Marty Nicolas C. M. , Grangeon Sylvain , Elkaïm Erik , Tournassat Christophe , Fauchet Clémence , Claret Francis
Published: May 2018

Amongst all cement phases, hydrated calcium aluminate (AFm) plays a major role in the retention of anionic species. Molybdenum (Mo), whose 93Mo isotope is considered a major steel activation product, will be released mainly under the form of MoO42− in a radioactive waste repository. Understanding its fate is of primary importance in a safety analysis of such disposal. This necessitates models that can both predict quantitatively the sorption of Mo by AFm and determine the nature of the sorption process (i.e., reversible adsorption or incorporation). This study investigated the Cl−/MoO42− exchange processes occurring in an AFm initially containing interlayer Cl in alkaline conditions using flow-through experiments. The evolution of the solid phase was characterized using an electron probe microanalyzer and synchrotron high-energy X-ray scattering. All data, together with their quantitative modeling, coherently indicated that Mo replaced Cl in the AFm interlayer. The structure of the interlayer is described with unprecedented atomic-scale detail based on a combination of real- and reciprocal-space analyses of total X-ray scattering data. In addition, modeling of several independent chemical experiments elucidated that Cl−/OH− exchange processes occur together with Cl−/MoO42− exchange. This competitive effect must be considered when determining the Cl−/MoO42− selectivity constant.
Ultranarrow-bandwidth filter based on a thermal EIT medium
Authors: Wang Gang , Wang Yu-Sheng , Huang Emily Kay , Hung Weilun , Chao Kai-Lin , Wu Ping-Yeh , Chen Yi-Hsin , Yu Ite A.
Published: May 2018

We present high-contrast electromagnetically-induced-transparency (EIT) spectra in a heated vapor cell of single isotope 87Rb atoms. The EIT spectrum has both high resonant transmission up to 67% and narrow linewidth of 1.1 MHz. We get rid of the possible amplification resulted from the effects of amplification without population inversion and four-wave mixing. Therefore, this high transmitted light is not artificial. The theoretical prediction of the probe transmission agrees well with the data and the experimental parameters can be derived reasonably from the model. Such narrow and high-contrast spectral profile can be employed as a high precision bandpass filter, which provides a significant advantage in terms of stability and tunability. The central frequency tuning range of the filter is larger than 100 MHz with out-of-band blocking ≥15 dB. This bandpass filter can effectively produce light fields with subnatural linewidth. Nonlinearity associating with the narrow-linewidth and high-contrast EIT profile can be very useful in the applications utilizing the EIT effect.
Evaluation of weed control efficacy and crop safety of the new HPPD-inhibiting herbicide-QYR301
Authors: Wang Hengzhi , Liu Weitang , Zhao Kongping , Yu Hui , Zhang Jia , Wang Jinxin
Published: May 2018

QYR301, 1,3-Dimethyl-1H-pyrazole-4-carboxylic acid 4-[2-chloro-3-(3,5-dimethyl-pyrazol-1-ylmethyl)-4-methanesulfonyl-benzoyl]-2,5-dimethyl-2H-pyrazol-3-yl ester, is a novel HPPD-inhibiting herbicide and was evaluated to provide a reference for post-emergence (POST) application under greenhouse and field conditions. The crop safety (180 and 360 g active ingredient (a.i.) ha−1 treatments) experiment revealed that wheat, paddy, garlic and corn were the only four crops without injury at both examined herbicide rates. The weed control efficacy (60 and 120 g a.i. ha−1) experiment showed that QYR301 exhibited high efficacy against many weeds, especially weeds infesting paddy fields. Furthermore, it is interesting that both susceptible and multiple herbicide resistant Echinochloa crus-galli (L.) Beauv. and Echinochloa phyllopogon (Stapf) Koss, two notorious weed species in paddy field, remained susceptible to QYR301. Further crop tolerance results indicated that 20 tested paddy hybrids displayed different levels of tolerance to QYR301, with the japonica paddy hybrids having more tolerance than indica paddy hybrids under greenhouse conditions. Results obtained from field experiments showed that QYR301 POST at 135 to 180 g a.i. ha−1 was recommended to provide satisfactory full-season control of E. crus-galli and Leptochloa chinensis (L.) Nees and to maximize rice yields. These findings indicate that QYR301 possesses great potential for the management of weeds in paddy fields.
Value of urinary KIM-1 and NGAL combined with serum Cys C for predicting acute kidney injury secondary to decompensated cirrhosis
Authors: Lei Lei , Li Liang Ping , Zeng Zhen , Mu Jing Xi , Yang Xue , Zhou Chao , Wang Zhi Lan , Zhang Hu
Published: May 2018

Urinary kidney injury molecule-1 (KIM-1), neutrophil gelatinase-associated lipocalin (NGAL), and serum cystatin C (Cys C) are biomarkers of acute kidney injury (AKI). However, the efficacy of combining these indices to diagnose decompensated cirrhosis is unknown. This study involved 150 patients divided into AKI and non-AKI, and healthy individuals. Urinary KIM-1 and NGAL, serum Cys and creatine, and glomerular filtration rate (GFR) were compared based on Child-Pugh liver function class. Urinary KIM-1 and NGAL concentrations and serum Cys C levels were significantly higher in patients with AKI secondary to decompensated cirrhosis than in those with AKI not secondary to decompensated cirrhosis (p < 0.01). These were significantly associated with higher kidney injury index stages (p < 0.01) and negatively correlated with GFR in secondary AKI patients. Urinary KIM-1 and NGAL and serum Cys C increased significantly and GFR decreased as Child-Pugh class of decompensated cirrhosis significantly increased (p < 0.05). SCr levels were significantly increased in Child-Pugh class C patients (p < 0.05). Urinary KIM-1, urinary NGAL, serum Cys C, and the combined detection factor, as screening indices, could aid in the early diagnosis of AKI secondary to decompensated cirrhosis.
Simultaneous cell disruption and semi-quantitative activity assays for high-throughput screening of thermostable L-asparaginases
Authors: Li Xu , Zhang Xian , Xu Shuqin , Zhang Hengwei , Xu Meijuan , Yang Taowei , Wang Li , Qian Haifeng , Zhang Huiling , Fang Haitian , Osire Tolbert , Rao Zhiming , Yang Shangtian
Published: May 2018

L-asparaginase, which catalyses the hydrolysis of L-asparagine to L-aspartate, has attracted the attention of researchers due to its expanded applications in medicine and the food industry. In this study, a novel thermostable L-asparaginase from Pyrococcus yayanosii CH1 was cloned and over-expressed in Bacillus subtilis 168. To obtain thermostable L-asparaginase mutants with higher activity, a robust high-throughput screening process was developed specifically for thermophilic enzymes. In this process, cell disruption and enzyme activity assays are simultaneously performed in 96-deep well plates. By combining error-prone PCR and screening, six brilliant positive variants and four key amino acid residue mutations were identified. Combined mutation of the four residues showed relatively high specific activity (3108 U/mg) that was 2.1 times greater than that of the wild-type enzyme. Fermentation with the mutant strain in a 5-L fermenter yielded L-asparaginase activity of 2168 U/mL.
Optimized delivery of siRNA into 3D tumor spheroid cultures in situ
Authors: Morgan R. G. , Chambers A. C. , Legge D. N. , Coles S. J. , Greenhough A. , Williams A. C.
Published: May 2018

3D tissue culture provides a physiologically relevant and genetically tractable system for studying normal and malignant human tissues. Despite this, gene-silencing studies using siRNA has proved difficult. In this study, we have identified a cause for why traditional siRNA transfection techniques are ineffective in eliciting gene silencing in situ within 3D cultures and proposed a simple method for significantly enhancing siRNA entry into spheroids/organoids. In 2D cell culture, the efficiency of gene silencing is significantly reduced when siRNA complexes are prepared in the presence of serum. Surprisingly, in both 3D tumour spheroids and primary murine organoids, the presence of serum during siRNA preparation rapidly promotes entry and internalization of Cy3-labelled siRNA in under 2 hours. Conversely, siRNA prepared in traditional low-serum transfection media fails to gain matrigel or spheroid/organoid entry. Direct measurement of CTNNB1 mRNA (encoding β-catenin) from transfected tumour spheroids confirmed a transient but significant knockdown of β-catenin when siRNA:liposome complexes were formed with serum, but not when prepared in the presence of reduced-serum media (Opti-MEM). Our studies suggest a simple modification to standard lipid-based transfection protocols facilitates rapid siRNA entry and transient gene repression, providing a platform for researchers to improve siRNA efficiency in established 3D cultures.
Mindfulness training induces structural connectome changes in insula networks
Authors: Sharp Paul B. , Sutton Bradley P. , Paul Erick J. , Sherepa Nikolai , Hillman Charles H. , Cohen Neal J. , Kramer Arthur F. , Prakash Ruchika Shaurya , Heller Wendy , Telzer Eva H. , Barbey Aron K.
Published: May 2018

Although mindfulness meditation is known to provide a wealth of psychological benefits, the neural mechanisms involved in these effects remain to be well characterized. A central question is whether the observed benefits of mindfulness training derive from specific changes in the structural brain connectome that do not result from alternative forms of experimental intervention. Measures of whole-brain and node-level structural connectome changes induced by mindfulness training were compared with those induced by cognitive and physical fitness training within a large, multi-group intervention protocol (n = 86). Whole-brain analyses examined global graph-theoretical changes in structural network topology. A hypothesis-driven approach was taken to investigate connectivity changes within the insula, which was predicted here to mediate interoceptive awareness skills that have been shown to improve through mindfulness training. No global changes were observed in whole-brain network topology. However, node-level results confirmed a priori hypotheses, demonstrating significant increases in mean connection strength in right insula across all of its connections. Present findings suggest that mindfulness strengthens interoception, operationalized here as the mean insula connection strength within the overall connectome. This finding further elucidates the neural mechanisms of mindfulness meditation and motivates new perspectives about the unique benefits of mindfulness training compared to contemporary cognitive and physical fitness interventions.
Imaging glutathione depletion in the rat brain using ascorbate-derived hyperpolarized MR and PET probes
Authors: Qin Hecong , Carroll Valerie N. , Sriram Renuka , Villanueva-Meyer Javier E. , von Morze Cornelius , Wang Zhen Jane , Mutch Christopher A. , Keshari Kayvan R. , Flavell Robert R. , Kurhanewicz John , Wilson David M.
Published: May 2018

Oxidative stress is a critical feature of several common neurologic disorders. The brain is well adapted to neutralize oxidative injury by maintaining a high steady-state concentration of small-molecule intracellular antioxidants including glutathione in astrocytes and ascorbic acid in neurons. Ascorbate-derived imaging probes for hyperpolarized 13C magnetic resonance spectroscopy and positron emission tomography have been used to study redox changes (antioxidant depletion and reactive oxygen species accumulation) in vivo. In this study, we applied these imaging probes to the normal rat brain and a rat model of glutathione depletion. We first studied hyperpolarized [1-13C]dehydroascorbate in the normal rat brain, demonstrating its robust conversion to [1-13C]vitamin C, consistent with rapid transport of the oxidized form across the blood-brain barrier. We next showed that the kinetic rate of this conversion decreased by nearly 50% after glutathione depletion by diethyl maleate treatment. Finally, we showed that dehydroascorbate labeled for positron emission tomography, namely [1-11C]dehydroascorbate, showed no change in brain signal accumulation after diethyl maleate treatment. These results suggest that hyperpolarized [1-13C]dehydroascorbate may be used to non-invasively detect oxidative stress in common disorders of the brain.
Induction of prolonged natural lifespans in mice exposed to acoustic environmental enrichment
Authors: Yamashita Yuichi , Kawai Norie , Ueno Osamu , Matsumoto Yui , Oohashi Tsutomu , Honda Manabu
Published: May 2018

We investigated the effect of acoustic environmental enrichment (EE) on the lifespans and behaviours of mice to the end of their natural lifespan in different acoustic environments. Acoustic EE induced a significantly prolonged natural lifespan (nearly 17% longer) and was associated with increased voluntary movements. However, no correlation between lifespan and voluntary movements was detected, suggesting that increased voluntary movements are not a primary cause of lifespan prolongation. Analyses of individual differences in lifespan demonstrated that lifespan extension induced by acoustic EE could be related to changes in social relationships (e.g., reduction of social conflict) among individuals kept within a cage. Therefore, an acoustic component may be an important factor inducing the positive effects of EE.
Inducible high-efficiency CRISPR-Cas9-targeted gene editing and precision base editing in African trypanosomes
Authors: Rico Eva , Jeacock Laura , Kovářová Julie , Horn David
Published: May 2018

The Cas9 endonuclease can be programmed by guide RNA to introduce sequence-specific breaks in genomic DNA. Thus, Cas9-based approaches present a range of novel options for genome manipulation and precision editing. African trypanosomes are parasites that cause lethal human and animal diseases. They also serve as models for studies on eukaryotic biology, including ‘divergent’ biology. Genome modification, exploiting the native homologous recombination machinery, has been important for studies on trypanosomes but often requires multiple rounds of transfection using selectable markers that integrate at low efficiency. We report a system for delivering tetracycline inducible Cas9 and guide RNA to Trypanosoma brucei. In these cells, targeted DNA cleavage and gene disruption can be achieved at close to 100% efficiency without further selection. Disruption of aquaglyceroporin (AQP2) or amino acid transporter genes confers resistance to the clinical drugs pentamidine or eflornithine, respectively, providing simple and robust assays for editing efficiency. We also use the new system for homology-directed, precision base editing; a single-stranded oligodeoxyribonucleotide repair template was delivered to introduce a single AQP2 - T791G/L264R mutation in this case. The technology we describe now enables a range of novel programmed genome-editing approaches in T. brucei that would benefit from temporal control, high-efficiency and precision.
On-wafer fabrication of cavity mirrors for InGaN-based laser diode grown on Si
Authors: He Junlei , Feng Meixin , Zhong Yaozong , Wang Jin , Zhou Rui , Gao Hongwei , Zhou Yu , Sun Qian , Liu Jianxun , Huang Yingnan , Zhang Shuming , Wang Huaibing , Ikeda Masao , Yang Hui
Published: May 2018

Direct bandgap III-V semiconductor lasers grown on silicon (Si) are highly desired for monolithic integration with Si photonics. Fabrication of semiconductor lasers with a Fabry–Pérot cavity usually includes facet cleavage, however, that is not compatible with on-chip photonic integration. Etching as an alternative approach holds a great advantage in preparing cavity mirrors with no need of breaking wafer into bars. However, gallium nitride (GaN) sidewalls prepared by dry etching often have a large roughness and etching damages, which would cause mirror loss due to optical scattering and carrier injection loss because of surface non-radiative recombination. A wet chemical polishing process of GaN sidewall facets formed by dry etching was studied in detail to remove the etching damages and smooth the vertical sidewalls. The wet chemical polishing technique combined with dry etching was successfully applied to the on-wafer fabrication of cavity mirrors, which enabled the realization of room temperature electrically injected InGaN-based laser diodes grown on Si.
Association of Blood Pressure with Fasting Blood Glucose Levels in Northeast China: A Cross-Sectional Study
Authors: Lv Yaogai , Yao Yan , Ye Junsen , Guo Xin , Dou Jing , Shen Li , Zhang Anning , Xue Zhiqiang , Yu Yaqin , Jin Lina
Published: May 2018

Hypertension and diabetes mellitus (DM) have become major public health issues, and previous studies have shown that there is an association between hypertension and DM. However, there is a lack of detailed information about this association. This study aimed to explore how different blood pressure (BP) levels were associated with fasting blood glucose (FBG) levels. A cross-sectional survey with adults aged 18 to 79 years was conducted in Jilin Province, China in 2012. Lambda-mu-sigma (LMS) was used to preliminarily explore the associations of BP with FBG. Quantile regression (QR) was performed to identify the specific associations by adjusting for confounding factors. The distributions of systolic blood pressure (SBP) (χ2 = 710.76, P < 0.001) and diastolic blood pressure (DBP) (χ2 = 460.20, P < 0.001) were different according to gender. LMS showed that the associations of BP with FBG became stronger when the FBG levels were close to 5.6 mmol/L. QR showed that FBG was positively associated with SBP (P30 to P90) and DBP (P20 to P90) in males. In females, FBG was positively associated with SBP from only P85 to P90. In summary, FBG was positively associated with BP in a gender-dependent manner.
Landau-Zener-Stückelberg Interferometry for Majorana Qubit
Authors: Wang Zhi , Huang Wen-Chao , Liang Qi-Feng , Hu Xiao
Published: May 2018

Stimulated by a recent experiment observing successfully two superconducting states with even- and odd-number of electrons in a nanowire topological superconductor as expected from the existence of two end Majorana quasiparticles (MQs) [Albrecht et al., Nature 531, 206 (2016)], we propose a way to manipulate Majorana qubit exploiting quantum tunneling effects. The prototype setup consists of two one-dimensional (1D) topological superconductors coupled by a tunneling junction which can be controlled by gate voltage. We show that the time evolution of superconducting phase difference at the junction under a voltage bias induces an oscillation in energy levels of the Majorana parity states, whereas the level-crossing is avoided by a small coupling energy of MQs in the individual 1D superconductors. This results in a Landau-Zener-Stückelberg (LZS) interference between the Majorana parity states. Adjusting pulses of bias voltage and gate voltage, one can construct a LZS interferometry which provides an arbitrary manipulation of the Majorana qubit.
Normalized spatial complexity analysis of neural signals
Authors: Jia Huibin , Li Yanwei , Yu Dongchuan
Published: May 2018

The spatial complexity of neural signals, which was traditionally quantified by omega complexity, varies inversely with the global functional connectivity level across distinct region-of-interests, thus provides a novel approach in functional connectivity analysis. However, the measures in omega complexity are sensitive to the number of neural time-series. Here, normalized spatial complexity was suggested to overcome the above limitation, and was verified by the functional near-infrared spectroscopy (fNIRS) data from a previous published autism spectrum disorder (ASD) research. By this new method, several conclusions consistent with traditional approaches on the pathological mechanisms of ASD were found, i.e., the prefrontal cortex made a major contribution to the hypo-connectivity of young children with ASD. Moreover, some novel findings were also detected (e.g., significantly higher normalized regional spatial complexities of bilateral prefrontal cortices and the variability of normalized local complexity differential of right temporal lobe, and the regional differences of measures in normalized regional spatial complexity), which could not be successfully detected via traditional approaches. These results confirmed the value of this novel approach, and extended the methodology system of functional connectivity. This novel technique could be applied to the neural signal of other neuroimaging techniques and other neurological and cognitive conditions.
Acrylamide acute neurotoxicity in adult zebrafish
Authors: Faria Melissa , Ziv Tamar , Gómez-Canela Cristian , Ben-Lulu Shani , Prats Eva , Novoa-Luna Karen Adriana , Admon Arie , Piña Benjamin , Tauler Romà , Gómez-Oliván Leobardo Manuel , Raldúa Demetrio
Published: May 2018

Acute exposure to acrylamide (ACR), a type-2 alkene, may lead to a ataxia, skeletal muscles weakness and numbness of the extremities in human and laboratory animals. In the present manuscript, ACR acute neurotoxicity has been characterized in adult zebrafish, a vertebrate model increasingly used in human neuropharmacology and toxicology research. At behavioral level, ACR-treated animals exhibited “depression-like” phenotype comorbid with anxiety behavior. At transcriptional level, ACR induced down-regulation of regeneration-associated genes and up-regulation of oligodendrocytes and reactive astrocytes markers, altering also the expression of genes involved in the presynaptic vesicle cycling. ACR induced also significant changes in zebrafish brain proteome and formed adducts with selected cysteine residues of specific proteins, some of them essential for the presynaptic function. Finally, the metabolomics analysis shows a depletion in the monoamine neurotransmitters, consistent with the comorbid depression and anxiety disorder, in the brain of the exposed fish.
Using Single Molecule mRNA Fluorescent in Situ Hybridization (RNA-FISH) to Quantify mRNAs in Individual Murine Oocytes and Embryos
Authors: Xie Fang , Timme Kelsey A. , Wood Jennifer R.
Published: May 2018

Changes in abundance of mRNAs during oocyte growth and maturation and during pre-implantation embryo development have been documented using quantitative real-time RT-PCR (qPCR), microarray analyses, and whole genome sequencing. However, these techniques require amplification of mRNAs, normalization using housekeeping genes, can be biased for abundant transcripts, and/or require large numbers of oocytes and embryos which can be difficult to acquire from mammalian species. We optimized a single molecule RNA fluorescence in situ hybridization (RNA-FISH) protocol, which amplifies fluorescence signal to detect candidate transcripts, for use with individual oocytes and embryos. Quantification using the software Localize showed patterns of Gdf9 and Pou5f1 mRNA expression in oocytes and embryos that were consistent with previously published data. Interestingly, low levels of Nanog mRNA were also accurately and reproducibly measured in oocytes and one- and two-cell embryos suggesting that RNA-FISH could be used to detect and quantify low abundance transcripts. Unlike other techniques, RNA-FISH is also able to detect changes in the localization patterns of mRNAs which may be used to monitor post-transcriptional regulation of a transcript. Thus, RNA-FISH represents an important technique to investigate potential mechanisms associated with the synthesis and stability of candidate mRNAs in mammalian oocytes and embryos.
Neuronal activity regulates DROSHA via autophagy in spinal muscular atrophy
Authors: Gonçalves Inês do Carmo G. , Brecht Johanna , Thelen Maximilian P. , Rehorst Wiebke A. , Peters Miriam , Lee Hyun Ju , Motameny Susanne , Torres-Benito Laura , Ebrahimi-Fakhari Darius , Kononenko Natalia L. , Altmüller Janine , Vilchez David , Sahin Mustafa , Wirth Brunhilde , Kye Min Jeong
Published: May 2018

Dysregulated miRNA expression and mutation of genes involved in miRNA biogenesis have been reported in motor neuron diseases including spinal muscular atrophy (SMA) and amyotrophic lateral sclerosis (ALS). Therefore, identifying molecular mechanisms governing miRNA expression is important to understand these diseases. Here, we report that expression of DROSHA, which is a critical enzyme in the microprocessor complex and essential for miRNA biogenesis, is reduced in motor neurons from an SMA mouse model. We show that DROSHA is degraded by neuronal activity induced autophagy machinery, which is also dysregulated in SMA. Blocking neuronal activity or the autophagy-lysosome pathway restores DROSHA levels in SMA motor neurons. Moreover, reducing DROSHA levels enhances axonal growth. As impaired axonal growth is a well described phenotype of SMA motor neurons, these data suggest that DROSHA reduction by autophagy may mitigate the phenotype of SMA. In summary, these findings suggest that autophagy regulates RNA metabolism and neuronal growth via the DROSHA/miRNA pathway and this pathway is dysregulated in SMA.
Polycomb Repressive Complex 2 attenuates the very high expression of the Arabidopsis gene NRT2.1
Authors: Bellegarde Fanny , Herbert Léo , Séré David , Caillieux Erwann , Boucherez Jossia , Fizames Cécile , Roudier François , Gojon Alain , Martin Antoine
Published: May 2018

PRC2 is a major regulator of gene expression in eukaryotes. It catalyzes the repressive chromatin mark H3K27me3, which leads to very low expression of target genes. NRT2.1, which encodes a key root nitrate transporter in Arabidopsis, is targeted by H3K27me3, but the function of PRC2 on NRT2.1 remains unclear. Here, we demonstrate that PRC2 directly targets and down-regulates NRT2.1, but in a context of very high transcription, in nutritional conditions where this gene is one of the most highly expressed genes in the transcriptome. Indeed, the mutation of CLF, which encodes a PRC2 subunit, leads to a loss of H3K27me3 at NRT2.1 and results, exclusively under permissive conditions for NRT2.1, in a further increase in NRT2.1 expression, and specifically in tissues where NRT2.1 is normally expressed. Therefore, our data indicates that PRC2 tempers the hyperactivity of NRT2.1 in a context of very strong transcription. This reveals an original function of PRC2 in the control of the expression of a highly expressed gene in Arabidopsis.
The significance of deformation mechanisms on the fracture behavior of phase reversion-induced nanostructured austenitic stainless steel
Authors: Misra R. D. K. , Injeti V. S. Y. , Somani M. C.
Published: May 2018

We describe here the relationship between grain structure, deformation mechanism and fracture characteristics in an austenitic stainless steel. This was accomplished using the novel concept of phase reversion that enabled a wide range of grain size from nanograined/ultrafine grained (NG/UFG) to coarse-grained (CG) regime to be obtained in a single material through change in temperature-time annealing sequence. In the NG/UFG structure, a marked increase in abundance of stacking faults (SFs) and twin density with strain was observed that led to a decrease in the average spacing between adjacent SFs, thus converting stacking faults into twins. Twinning in NG/UFG structure involved partial dislocations and their interaction with the grain boundaries, including SF overlapping and the coordinated nucleation of partial dislocations from the grain boundaries. The plastic zone in the NG/UFG structure resembled a network knitted by the intersecting twins and SFs. With SFE ~30 mJ/m2, the minimum stress for twin nucleation was ~250 MPa for the experiment steel and the corresponding optimal grain size (dop) wa ~120 nm. In contrast, in the CG structure, strain induced martensite formation was the deformation mechanism. The difference in the deformation mechanism led to a clear distinction in the fracture behavior from striated fracture in high strength-high ductility NG/UFG alloy to microvoid coalescence in the low strength-high ductility CG counterpart. The underlying reason for the change in fracture behavior was consistent with change in deformation mechanism from nanoscale twinning in NG/UFG alloy to strain-induced martensite in the CG alloy, which is related to change in the stability of austenite with grain size. An analysis of critical shear stress required to initiate twinning partial dislocations in comparison to that required to nucleate shear bands is presented. The appearance of striated fracture in the NG/UFG alloy suggests a quasi-static step wise crack growth process.
Components in Lentinus edodes mushroom with anti-biofilm activity directed against bacteria involved in caries and gingivitis
Authors: Papetti Adele , Signoretto Caterina , Spratt David A. , Pratten Jonathan , Lingström Peter , Zaura Egija , Ofek Itzhak , Wilson Michael , Pruzzo Carla , Gazzani Gabriella
Published: May 2018

The present study investigated the compounds present in the low molecular mass fraction of Lentinus edodes mushroom (shiitake) extract and their anti-virulence activity against oral pathogens.
A study on the preparation of pitch-based high-strength columnar activated carbon and mechanism of phenol adsorption from aqueous solution
Authors: Yao Peng , Cen Jianmeng , Fang Mengxiang , Wang Tao , Wang Qinhui
Published: May 2018

Coal tar pitch was ground into powder and hydroformed with high pressure. After pre-oxidation, the pitch was activated by CO2 at high temperature.
A connection between living liquid crystals and electrokinetic phenomena in nematic fluids
Authors: Conklin Christopher , Viñals Jorge , Valls Oriol T.
Published: May 2018

We develop a formal analogy between configurational stresses in physically distinct systems, and study the flows that they induce when the configurations of interest include topological defects.