bluuebunny/crossref_metadata_2025 huggingface dataset:
Sounding-rocket microgravity experiments on alumina dust
Authors: Ishizuka Shinnosuke , Kimura Yuki , Sakon Itsuki , Kimura Hiroshi , Yamazaki Tomoya , Takeuchi Shinsuke , Inatomi Yuko
Published: September 2018

Alumina (Al2O3) is believed to be the first major condensate to form in the gas outflow from oxygen-rich evolved stars because of the refractoriness and that α-Al2O3 (corundum, most stable polymorph) is a potential origin of a 13 μm feature that appears close to stars. However, no one has directly reproduced the 13 μm feature experimentally, and it has remained as a noteworthy unidentified infrared band. Here, we report nucleation experiments on Al2O3 nanoparticles monitored by a specially designed infrared spectrometer in the microgravity environment of a sounding rocket. The conditions approximate to those around asymptotic giant branch (AGB) stars. The measured spectra of the nucleated Al2O3 show a sharp feature at a wavelength of 13.55 μm and comparable in width to that observed near oxygen-rich AGB stars. Our finding that α-Al2O3 nucleates under certain condition provides a solid basis to elaborate condensation models of dust around oxygen-rich evolved stars.
Insight into anaerobic methanotrophy from 13C/12C- amino acids and 14C/12C-ANME cells in seafloor microbial ecology
Authors: Takano Yoshinori , Chikaraishi Yoshito , Imachi Hiroyuki , Miyairi Yosuke , Ogawa Nanako O. , Kaneko Masanori , Yokoyama Yusuke , Krüger Martin , Ohkouchi Naohiko
Published: September 2018

Oceanic methane from global deep-sea sediment is largely consumed through microbially mediated sulfate-coupled oxidation, resulting in 13C-depleted cell biomass of anaerobic methanotrophic archaea (ANME). The general ecological importance of subseafloor ANME has been well recognized in the last two decades. However, the crucial biochemical pathways for the overall anaerobic oxidation of methane (AOM) still remain enigmatic. Here, methanotrophic pathways were analyzed to trace 13C-depleted amino acid biosynthesis in two clades of ANME (ANME-1 and ANME-2) from the Black Sea. Compound-specific analysis of ANME-dominated microbial mats showed a significant 13C-depletion trend in association with increasing carbon numbers in protein-derived amino acid families (e.g., the pyruvate family in the order of alanine, valine, isoleucine and leucine was down to −114‰). This result indicates a stepwise elongation of 13C-depleted carbon during amino acid biosynthesis. The overall results suggest that intracellular protein amino acids and the most 13C-depleted signature of leucine, which has a specific branched-chain structure, are potentially propagated as isoprenoid precursor molecules into archaeal biosynthesis, resulting in the extremely 13C- and 14C-depleted nature of ANME cells in the deep microbial oasis.
Optogenetic Peripheral Nerve Immunogenicity
Authors: Maimon Benjamin E. , Diaz Maurizio , Revol Emilie C. M. , Schneider Alexis M. , Leaker Ben , Varela Claudia E. , Srinivasan Shriya , Weber Matthew B. , Herr Hugh M.
Published: September 2018

Optogenetic technologies have been the subject of great excitement within the scientific community for their ability to demystify complex neurophysiological pathways in the central (CNS) and peripheral nervous systems (PNS). The excitement surrounding optogenetics has also extended to the clinic with a trial for ChR2 in the treatment of retinitis pigmentosa currently underway and additional trials anticipated for the near future. In this work, we identify the cause of loss-of-expression in response to transdermal illumination of an optogenetically active peroneal nerve following an anterior compartment (AC) injection of AAV6-hSyn-ChR2(H134R) with and without a fluorescent reporter. Using Sprague Dawley Rag2−/− rats and appropriate controls, we discover optogenetic loss-of-expression is chiefly elicited by ChR2-mediated immunogenicity in the spinal cord, resulting in both CNS motor neuron death and ipsilateral muscle atrophy in both low and high Adeno-Associated Virus (AAV) dosages. We further employ pharmacological immunosuppression using a slow-release tacrolimus pellet to demonstrate sustained transdermal optogenetic expression up to 12 weeks. These results suggest that all dosages of AAV-mediated optogenetic expression within the PNS may be unsafe. Clinical optogenetics for both PNS and CNS applications should take extreme caution when employing opsins to treat disease and may require concurrent immunosuppression. Future work in optogenetics should focus on designing opsins with lesser immunogenicity.
Ratio of mitochondrial to nuclear DNA affects contamination estimates in ancient DNA analysis
Authors: Furtwängler Anja , Reiter Ella , Neumann Gunnar U. , Siebke Inga , Steuri Noah , Hafner Albert , Lösch Sandra , Anthes Nils , Schuenemann Verena J. , Krause Johannes
Published: September 2018

In the last decade, ancient DNA research has grown rapidly and started to overcome several of its earlier limitations through Next-Generation-Sequencing (NGS). Among other advances, NGS allows direct estimation of sample contamination from modern DNA sources. First NGS-based approaches of estimating contamination measured heterozygosity. These measurements, however, could only be performed on haploid genomic regions, i.e. the mitochondrial genome or male X chromosomes, but provided no measures of contamination in the nuclear genome of females with their two X chromosomes. Instead, female nuclear contamination is routinely extrapolated from mitochondrial contamination estimates, but it remains unclear if this extrapolation is reliable and to what degree variation in mitochondrial to nuclear DNA ratios affects this extrapolation. We therefore analyzed ancient DNA from 317 samples of different skeletal elements from multiple sites, spanning a temporal range from 7,000 BP to 386 AD. We found that the mitochondrial to nuclear DNA (mt/nc) ratio negatively correlates with an increase in endogenous DNA content and strongly influenced mitochondrial and nuclear contamination estimates in males. The ratio of mt to nc contamination estimates remained stable for overall mt/nc ratios below 200, as found particularly often in petrous bones but less in other skeletal elements and became more variable above that ratio.
Altitudinal dependence of PCBs and PBDEs in soil along the two sides of Mt. Sygera, southeastern Tibetan Plateau
Authors: Meng Wenying , Wang Pu , Yang Ruiqiang , Sun Huizhong , Matsiko Julius , Wang Dou , Zuo Peijie , Li Yingming , Zhang Qinghua , Jiang Guibin
Published: September 2018

Surface soil samples were collected from Mt. Sygera in the southeast of Tibetan Plateau to investigate the altitudinal distribution of PCBs and PBDEs along the two sides of the mountain. The average concentrations of PCBs and PBDEs were 177 pg g−1 dw and 15 pg g−1 dw, respectively. The relationships between the log-transformed TOC-normalized concentrations and the altitudes showed different trends on the two sides. On the windward side, there was a positive correlation for the heavier PCBs; while on the leeward side, the concentrations increased and then decreased for PCBs and PBDEs at the altitude of 4100–4200 m, corresponding to the change in vegetation. The observed discrepancy on the two sides of the mountain demonstrated different key factors associated with precipitation and the forest canopy. Additionally, values of windward-leeward Enrichment Factors (W/L EFs) for the heavier PCB congeners (PCB-138, 153, and -180) were an order of magnitude higher in sites above 4200 m, which also suggested that vegetation played an important role in the altitudinal accumulation of POPs in soil. This is one of the very few studies that have revealed the differences in altitudinal accumulation of POPs along the two sides of a mountain.
RETRACTED ARTICLE: Visualising the dynamics of live pancreatic microtumours self-organised through cell-in-cell invasion
Authors: Miyatake Yukiko , Kuribayashi-Shigetomi Kaori , Ohta Yusuke , Ikeshita Shunji , Subagyo Agus , Sueoka Kazuhisa , Kakugo Akira , Amano Maho , Takahashi Toshiyuki , Okajima Takaharu , Kasahara Masanori
Published: September 2018

Pancreatic ductal adenocarcinoma (PDAC) reportedly progresses very rapidly through the initial carcinogenesis stages including DNA damage and disordered cell death. However, such oncogenic mechanisms are largely studied through observational diagnostic methods, partly because of a lack of live in vitro tumour imaging techniques. Here we demonstrate a simple live-tumour in vitro imaging technique using micro-patterned plates (micro/nanoplates) that allows dynamic visualisation of PDAC microtumours. When PDAC cells were cultured on a micro/nanoplate overnight, the cells self-organised into non-spheroidal microtumours that were anchored to the micro/nanoplate through cell-in-cell invasion. This self-organisation was only efficiently induced in small-diameter rough microislands. Using a time-lapse imaging system, we found that PDAC microtumours actively stretched to catch dead cell debris via filo/lamellipoedia and suction, suggesting that they have a sophisticated survival strategy (analogous to that of starving animals), which implies a context for the development of possible therapies for PDACs. The simple tumour imaging system visualises a potential of PDAC cells, in which the aggressive tumour dynamics reminds us of the need to review traditional PDAC pathogenesis.
Exploring gravity with the MIGA large scale atom interferometer
Authors: Canuel B. , Bertoldi A. , Amand L. , Pozzo di Borgo E. , Chantrait T. , Danquigny C. , Dovale Álvarez M. , Fang B. , Freise A. , Geiger R. , Gillot J. , Henry S. , Hinderer J. , Holleville D. , Junca J. , Lefèvre G. , Merzougui M. , Mielec N. , Monfret T. , Pelisson S. , Prevedelli M. , Reynaud S. , Riou I. , Rogister Y. , Rosat S. , Cormier E. , Landragin A. , Chaibi W. , Gaffet S. , Bouyer P.
Published: September 2018

We present the MIGA experiment, an underground long baseline atom interferometer to study gravity at large scale. The hybrid atom-laser antenna will use several atom interferometers simultaneously interrogated by the resonant mode of an optical cavity. The instrument will be a demonstrator for gravitational wave detection in a frequency band (100 mHz–1 Hz) not explored by classical ground and space-based observatories, and interesting for potential astrophysical sources. In the initial instrument configuration, standard atom interferometry techniques will be adopted, which will bring to a peak strain sensitivity of $${\bf{2}}\cdot {\bf{1}}{{\bf{0}}}^{-{\bf{13}}}/\sqrt{{\bf{H}}{\bf{z}}}$$
2
⋅
1

0

−
13

/

H
z

at 2 Hz. This demonstrator will enable to study the techniques to push further the sensitivity for the future development of gravitational wave detectors based on large scale atom interferometers. The experiment will be realized at the underground facility of the Laboratoire Souterrain à Bas Bruit (LSBB) in Rustrel–France, an exceptional site located away from major anthropogenic disturbances and showing very low background noise. In the following, we present the measurement principle of an in-cavity atom interferometer, derive the method for Gravitational Wave signal extraction from the antenna and determine the expected strain sensitivity. We then detail the functioning of the different systems of the antenna and describe the properties of the installation site.
Salicylic acid in Populus tomentosa is a remote signalling molecule induced by Botryosphaeria dothidea infection
Authors: Li Yong-xia , Zhang Wei , Dong Hui-xia , Liu Zhen-yu , Ma Jian , Zhang Xing-yao
Published: September 2018

The salicylic acid (SA) plays a critical role during the establishment of systemic acquired resistance (SAR) in uninfected plant tissues after localised exposure to a pathogen. Here, we studied SA in Populus tomentosa infected by the plant pathogen Botryosphaeria dothidea. The accumulation of SA and methyl salicylate (MeSA) occurred in chronological order in P. tomentosa. The SA and MeSA contents were greater at infected than uninfected sites. Additionally, a gene expression analysis indicated that SA might be accumulated by phenylalanine ammonialyase (PAL) and converted to MeSA by SA carboxyl methyltransferase (SAMT), while MeSA might convert to SA by SA-binding protein 2 (SABP2). The expressions of SAMT at infected sites and SABP2 at uninfected sites, respectively, were significantly up-regulated. Thus, SA might be converted to MeSA at infected sites and transported as a signalling molecule to uninfected sites, where it is converted to SA for SAR. Moreover, the expressions of pathogenesis-related genes PR-1, PR-2 and PR-5 in P. tomentosa were up-regulated by the B. dothidea infection. Our study determined that variations in SA and MeSA contents occur at infected and uninfected sites in poplar after pathogen infection and contributed to the remote signals for poplar SAR.
Exploration and application of a highly sensitive bis(salamo)-based fluorescent sensor for B4O72− in water-containing systems and living cells
Authors: Pu Lu-Mei , Li Xiao-Yan , Hao Jing , Sun Yin-Xia , Zhang Yang , Long Hai-Tao , Dong Wen-Kui
Published: September 2018

A highly selective fluorescent sensor H4L based on a bis(salamo)-type compound with two N2O2 chelating moieties as ionophore was successfully developed. Sensor H4L was found to have excellent selectivity for B4O72− over many other anions (Br−, CI−, CN−, CO32−, HCO3−, H2PO4−, HSO4−, NO3−, OAc−, S2O3−, SCN−, SO42−, Hcy (homocysteine) and H2O2), and it exhibited an approximately 150-fold enhancement of the fluorescence response to B4O72− in Tris-HCl buffer (DMF/H2O = 9:1, v/v, pH = 7) solutions. Significantly, its fluorescence intensity was enhanced in a linear fashion with increasing concentrations of B4O72−. The detection limit of sensor H4L towards B4O72− was 8.61 × 10−7 M. The test strips could conveniently, efficiently and simply detect B4O72− ions in Tris-HCl buffer (DMF/H2O = 9:1, v/v, pH = 7) solutions. Furthermore, sensor H4L showed excellent membrane permeability in living cells, and it was successfully used to monitor intracellular B4O72− by confocal luminescence imaging.
Mutagen-induced phytotoxicity in maize seed germination is dependent on ROS scavenging capacity
Authors: Zhang Yifei , Shi Haojie , Deng Benliang
Published: September 2018

Ethidium bromide (EB) and acridine orange (AO) bind to nucleic acids and are thus considered as potential mutagens. In this study, the effects of EB and AO on the germination behaviours of white, yellow, red, and purple maize seeds were investigated. The results indicate that low concentrations of EB (50 μg mL−1) and AO (500 μg mL−1) promote germination, particularly for the white and yellow seeds. However, high concentrations of EB (0.5 mg mL−1) and AO (5 mg mL−1) significantly inhibit germination, with the level of inhibition decreasing in the following order: white > yellow > red > purple. In addition, EB and AO induce H2O2 production in a concentration-dependent manner. The effects of these mutagens on seed germination were partly reversed by dimethyl thiourea, a scavenger of reactive oxygen species (ROS), and diphenylene iodonium (DPI), an inhibitor of NADPH oxidase, while the effects were enhanced by treatment with H2O2 and 3-amino-1,2,4-triazole, a specific inhibitor of catalase. In addition, AO and EB profoundly increased NADPH oxidase activities in germinating seeds. The treatment of seeds with EB and AO did not affect the growth or drought tolerance of the resultant seedlings. The findings suggest that the mechanism of mutagen toxicity is related to the induction of ROS production.
Association between Subcortical Morphology and Cerebral White Matter Energy Metabolism in Neonates with Congenital Heart Disease
Authors: Gertsvolf Nina , Votava-Smith Jodie K. , Ceschin Rafael , del Castillo Sylvia , Lee Vince , Lai Hollie A. , Bluml Stefan , Paquette Lisa , Panigrahy Ashok
Published: September 2018

Complex congenital heart disease (CHD) is associated with neurodevelopmental impairment, the mechanism of which is unknown. Cerebral cortical dysmaturation in CHD is linked to white matter abnormalities, including developmental vulnerability of the subplate, in relation to oxygen delivery and metabolism deficits. In this study, we report associations between subcortical morphology and white matter metabolism in neonates with CHD using quantitative magnetic resonance imaging (MRI) and spectroscopy (MRS). Multi-modal brain imaging was performed in three groups of neonates close to term-equivalent age: (1) term CHD (n = 56); (2) preterm CHD (n = 37) and (3) preterm control group (n = 22). Thalamic volume and cerebellar transverse diameter were obtained in relation to cerebral metrics and white matter metabolism. Short echo single-voxel MRS of parietal and frontal white matter was used to quantitate metabolites related to brain maturation (n-acetyl aspartate [NAA], choline, myo-inositol), neurotransmitter (glutamate), and energy metabolism (glutamine, citrate, creatine and lactate). Multi-variate regression was performed to delineate associations between subcortical morphological measurements and white matter metabolism controlling for age and white matter injury. Reduced thalamic volume, most pronounced in the preterm control group, was associated with increased citrate levels in all three group in the parietal white matter. In contrast, reduced cerebellar volume, most pronounced in the preterm CHD group, was associated with reduced glutamine in parietal grey matter in both CHD groups. Single ventricle anatomy, aortic arch obstruction, and cyanotic lesion were predictive of the relationship between reduced subcortical morphometry and reduced GLX (particularly glutamine) in both CHD cohorts (frontal white matter and parietal grey matter). Subcortical morphological associations with brain metabolism were also distinct within each of the three groups, suggesting these relationships in the CHD groups were not directly related to prematurity or white matter injury alone. Taken together, these findings suggest that subplate vulnerability in CHD is likely relevant to understanding the mechanism of both cortical and subcortical dysmaturation in CHD infants. Future work is needed to link this potential pattern of encephalopathy of CHD (including the constellation of grey matter, white matter and brain metabolism deficits) to not only abnormal fetal substrate delivery and oxygen conformance, but also regional deficits in cerebral energy metabolism.
Light-cured polymer electrodes for non-invasive EEG recordings
Authors: de Camp Nora Vanessa , Kalinka Gerhard , Bergeler Jürgen
Published: September 2018

We invented the first non-metallic, self-adhesive and dry biosignalling electrode. The PEDOT polymer electrode changes its aggregate state and conductivity by a light curing procedure. The electrode can be applied as a gel underneath hair without shaving. With the aid of blue light, the electrode can be hardened within a few seconds at the desired location on the scalp. The cured polymer electrode is highly conductive and can be applied on a very small location. Unlike other EEG electrodes, our electrode does not lose conductivity upon drying. Furthermore, our electrode strongly bonds to skin and does not require any additional adhesive. Short circuits due to an outflow of gel are prevented with this technique. Therefore, the PEDOT polymer electrode is extremely well suited for applications that, up to now, have been challenging, such as non-invasive EEG recordings from awake and freely moving animals, EEG recordings from preterm babies in the neonatal intensive care unit or long-term recordings in the case of sleep monitoring or epilepsy diagnostics. We addressed two technical questions in this work. First, is the EEG recorded with polymer electrodes comparable to a standard EEG? Second, is it possible to record full-band EEGs with our electrodes?
N-Phenylquinazolin-2-amine Yhhu4952 as a novel promotor for oligodendrocyte differentiation and myelination
Authors: Yu Xueli , Cheng Gang , Zhang Lei , Zhang Yu , Wang Qing , Zhao Mengxue , Zeng Limin , Hu Youhong , Feng Linyin
Published: September 2018

Oligodendrocytes are a type of glial cells that ensheath multiple neuronal axons and form myelin. Under pathological conditions, such as multiple sclerosis (MS), inflammatory damage to myelin and oligodendrocytes leads to demyelination. Although the demyelinated regions can partially resolve functional deficits through remyelination, however, as the disease progresses, remyelination typically becomes incomplete and ultimately fails. One possible explanation for this failure is the activation of the Notch pathway in MS lesions, which impedes oligodendrocyte precursor cells (OPCs) at maturation. This leads to a potential target for remyelination. Here, we have identified a compound Yhhu4952 that promoted the maturation of cultured OPCs in a dose-dependent and time-dependent manner. Neonatal rats showed a significant increase in the expression of myelin basic protein (MBP) and the prevalence of mature oligodendrocytes in the corpus callosum after Yhhu4952 treatment. The compound was also effective in promoting remyelination in cuprizone-induced demyelination model and improving severity scores in experimental autoimmune encephalomyelitis (EAE) model. Mechanism studies revealed that Yhhu4952 promotes OPC differentiation through the inhibition of the Jagged1-Notch1 pathway. These findings suggest Yhhu4952 is potentially useful for proceeding oligodendrocyte differentiation and remyelination.
Green microalgae in marine coastal waters: The Ocean Sampling Day (OSD) dataset
Authors: Tragin Margot , Vaulot Daniel
Published: September 2018

The ecology and distribution of green phytoplankton (Chlorophyta) in the ocean is poorly known because most studies have focused on groups with large cell size such as diatoms or dinoflagellates that are easily recognized by traditional techniques such as microscopy. The Ocean Sampling Day (OSD) project sampled surface waters quasi-simultaneously at 141 marine locations, mostly in coastal waters. The analysis of the 18S V4 region OSD metabarcoding dataset reveals that Chlorophyta are ubiquitous and can be locally dominant in coastal waters. Chlorophyta represented 29% of the global photosynthetic reads (Dinoflagellates excluded) and their contribution was especially high at oligotrophic stations (up to 94%) and along the European Atlantic coast. Mamiellophyceae dominated most coastal stations. At some coastal stations, they were replaced by Chlorodendrophyceae, Ulvophyceae, Trebouxiophyceae or Chlorophyceae as the dominating group, while oligotrophic stations were dominated either by Chloropicophyceae or the uncultured prasinophytes clade IX. Several Chlorophyta classes showed preferences in terms of nitrate concentration, distance to the coast, temperature and salinity. For example, Chlorophyceae preferred cold and low salinity coastal waters, and prasinophytes clade IX warm, high salinity, oligotrophic oceanic waters.
Thiophene-based porous organic networks for volatile iodine capture and effectively detection of mercury ion
Authors: Liu Minghan , Yao Chan , Liu Chunbo , Xu Yanhong
Published: September 2018

A series of conjugated microporous polymers containing thiophene-moieties (SCMP-COOH@1-3) was obtained by a homo-coupling polymerization reaction. Then the SCMP-COOH@1-3 were directly pyrolyzed without any templates to synthesize the porous carbon networks, named as SCMP-600@1, 2 and 3. SCMP-600@1-3 possess moderate BET surface area of 362–642 m2 g−1, have a permanent porous structure and plenty of sulfur and oxygen units in the skeletons as effective sorption sites, and display a high absorption performance for iodine vapour with an uptake up to 204 wt.%. In addition, SCMP-COOH@1-3 polymers can be used to effectively detect mercury ion from ethanol-water solution. Interestingly, under the same concentration of Hg2+ conditions, the detection ability of mercury ion of porous materials increased with the increase of the pore volumes and the specific surface.
Ag+ doped into azo-linked conjugated microporous polymer for volatile iodine capture and detection of heavy metal ions
Authors: Liu Minghan , Yao Chan , Liu Chunbo , Xu Yanhong
Published: September 2018

We herein report the construction of a novel azo-linked conjugated microporous polymers (Ag@AzoTPE-CMP), which possesses permanent porous structure and Ag+ loading up of 7.62% in the skeleton as effective sorption sites. Ag@AzoTPE-CMP shows considerable adsorption capacity of iodine of 202 wt% in iodine vapor at 350 K. In addition, Ag@AzoTPE-CMP can effectively remove heavy ions from ethanol-water solution.
Laser surface structuring of diamond with ultrashort Bessel beams
Authors: Kumar Sanjeev , Eaton Shane M. , Bollani Monica , Sotillo Belén , Chiappini Andrea , Ferrari Maurizio , Ramponi Roberta , Di Trapani Paolo , Jedrkiewicz Ottavia
Published: September 2018

We investigate the effect of ultrafast laser surface machining on a monocrystalline synthetic diamond sample by means of pulsed Bessel beams. We discuss the differences of the trench-like microstructures generated in various experimental conditions, by varying the beam cone angle, the energy and pulse duration, and we present a brief comparison of the results with those obtained with the same technique on a sapphire sample. In diamond, we obtain V-shaped trenches whose surface width varies with the cone angle, and which are featured by micrometer sized channels having depths in the range of 10–20 μm. By laser writing crossed trenches we are also able to create and tailor on the diamond surface pillar-like or tip-like microstructures potentially interesting for large surface functionalization, cells capturing and biosensing.
MicroRNA-194-5p Levels Decrease during Deep Hypothermic Circulatory Arrest
Authors: Wang Xiaohua , You Zerong , Zhao Guoguang , Wang Tianlong
Published: September 2018

Hypothermia has been reported to be effective in protecting the brain in various clinical conditions, including resuscitation after cardiac arrest and complex cardiovascular surgery, and is considered to be a promising therapy for stroke. The present study aimed to confirm the pivotal role that miRNA-194-5p plays in deep hypothermia circulation arrest. On the basis of reductions in expression of miR-194-5p in the circulation of 21 aortic dissection patients who underwent deep hypothermia circulatory arrest, the specific expression, target, and function of miR-194-5p was investigated using primary neuron culture, polymerase chain reaction, in situ hybridization, and flow cytometry methods. Our results showed that miR-194-5p expression was significantly downregulated in hypothermia oxygen glucose deprivation-treated neurons in vitro. Cortical neurons transfected with miR-194-5p mimic exhibited increased death due to oxygen-glucose deprivation. MiR-194-5p mediated the regulation of neuronal death, which involves the downregulation of the specific target protein SUMO2, which is crucial to ischemia tolerance. Collectively, these data highlight the unique role of miR-194-5p in mediating the deep hypothermia circulation arrest response via the regulation of SUMO2. These findings suggest that miR-194-5p could be a potential therapeutic target for intervention in ischemic disease.
Pretreatment Identification of Head and Neck Cancer Nodal Metastasis and Extranodal Extension Using Deep Learning Neural Networks
Authors: Kann Benjamin H. , Aneja Sanjay , Loganadane Gokoulakrichenane V. , Kelly Jacqueline R. , Smith Stephen M. , Decker Roy H. , Yu James B. , Park Henry S. , Yarbrough Wendell G. , Malhotra Ajay , Burtness Barbara A. , Husain Zain A.
Published: September 2018

Identification of nodal metastasis and tumor extranodal extension (ENE) is crucial for head and neck cancer management, but currently only can be diagnosed via postoperative pathology. Pretreatment, radiographic identification of ENE, in particular, has proven extremely difficult for clinicians, but would be greatly influential in guiding patient management. Here, we show that a deep learning convolutional neural network can be trained to identify nodal metastasis and ENE with excellent performance that surpasses what human clinicians have historically achieved. We trained a 3-dimensional convolutional neural network using a dataset of 2,875 CT-segmented lymph node samples with correlating pathology labels, cross-validated and fine-tuned on 124 samples, and conducted testing on a blinded test set of 131 samples. On the blinded test set, the model predicted ENE and nodal metastasis each with area under the receiver operating characteristic curve (AUC) of 0.91 (95%CI: 0.85–0.97). The model has the potential for use as a clinical decision-making tool to help guide head and neck cancer patient management.
Using a Classifier Fusion Strategy to Identify Anti-angiogenic Peptides
Authors: Zhang Lina , Yang Runtao , Zhang Chengjin
Published: September 2018

Anti-angiogenic peptides perform distinct physiological functions and potential therapies for angiogenesis-related diseases. Accurate identification of anti-angiogenic peptides may provide significant clues to understand the essential angiogenic homeostasis within tissues and develop antineoplastic therapies. In this study, an ensemble predictor is proposed for anti-angiogenic peptide prediction by fusing an individual classifier with the best sensitivity and another individual one with the best specificity. We investigate predictive capabilities of various feature spaces with respect to the corresponding optimal individual classifiers and ensemble classifiers. The accuracy and Matthew’s Correlation Coefficient (MCC) of the ensemble classifier trained by Bi-profile Bayes (BpB) features are 0.822 and 0.649, respectively, which represents the highest prediction results among the investigated prediction models. Discriminative features are obtained from BpB using the Relief algorithm followed by the Incremental Feature Selection (IFS) method. The sensitivity, specificity, accuracy, and MCC of the ensemble classifier trained by the discriminative features reach up to 0.776, 0.888, 0.832, and 0.668, respectively. Experimental results indicate that the proposed method is far superior to the previous study for anti-angiogenic peptide prediction.
Overexpression of an auxin receptor OsAFB6 significantly enhanced grain yield by increasing cytokinin and decreasing auxin concentrations in rice panicle
Authors: He Qin , Yang Lin , Hu Wei , Zhang Jia , Xing Yongzhong
Published: September 2018

Auxin plays critical roles in many developmental processes of plants. The auxin signaling pathway is a series of plant responses to auxin stimuli. However, the functions of many genes in this pathway are still obscure. As auxin receptors,TIR/AFBfamily genes encode F-Box proteins that directly bind auxin and then transduce the stimulus through the signaling pathway. In this paper, we generated an overexpression line ofAuxin-signaling F-Box 6(OsAFB6) in rice, which largely delayed heading, greatly increased spikelets per panicle and primary branch number and ultimately enhanced grain yield by 50%.OsAFB6is preferentially expressed in young tissues with stronger meristem activities and suppresses flowering by upregulatingOsRR1and downregulatingEhd1expression levels. Overexpression ofOsAFB6delayed heading, increased cytokinin (CK) by suppressing the expression level ofGn1aand simultaneously decreased the IAA concentration in the young panicle, which promoted inflorescence meristem development and resulted in large panicles with more spikelets per panicle, primary branches and increased grain yield. It would be a beneficial strategy to generate lines with varied expression levels ofOsAFB6to breed high-yielding cultivars for specific regions that can fully utilize the local sunlight and temperature resources.
Pseudomonas aeruginosa ExoS Induces Intrinsic Apoptosis in Target Host Cells in a Manner That is Dependent on its GAP Domain Activity
Authors: Kaminski Amber , Gupta Kajal H. , Goldufsky Josef W. , Lee Ha Won , Gupta Vineet , Shafikhani Sasha H.
Published: September 2018

Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen that causes serious infections in immunocompromised individuals and cystic fibrosis patients. ExoS and ExoT are two homologous bifunctional Type III Secretion System (T3SS) virulence factors that induce apoptosis in target host cells. They possess a GTPase Activating Protein (GAP) domain at their N-termini, which share ~76% homology, and an ADP-ribosyltransferase (ADPRT) domain at their C-termini, which target non-overlapping substrates. Both the GAP and the ADPRT domains contribute to ExoT’s cytotoxicity in target epithelial cells, whereas, ExoS-induced apoptosis is reported to be primarily due to its ADPRT domain. In this report, we demonstrate that ExoS/GAP domain is both necessary and sufficient to induce mitochondrial apoptosis. Our data demonstrate that intoxication with ExoS/GAP domain leads to enrichment of Bax and Bim into the mitochondrial outer-membrane, disruption of mitochondrial membrane and release of and cytochrome c into the cytosol, which activates initiator caspase-9 and effector caspase-3, that executes cellular death. We posit that the contribution of the GAP domain in ExoS-induced apoptosis was overlooked in prior studies due to its slower kinetics of cytotoxicity as compared to ADPRT. Our data clarify the field and reveal a novel virulence function for ExoS/GAP as an inducer of apoptosis.
Sensitive and rapid quantification of exosomes by fusing luciferase to exosome marker proteins
Authors: Hikita Tomoya , Miyata Mamiko , Watanabe Risayo , Oneyama Chitose
Published: September 2018

Exosomes have emerged as important mediators of intercellular communication. Although their modes of action have been elucidated, the molecular mechanisms underlying their secretion, sorting of molecules, uptake into recipient cells, and biological distribution in vivo remain elusive. Here, we present a novel system for quantifying secreted exosomes by introducing ectopic or CRISPR/Cas9-mediated knock-in of luciferase-fusion exosome markers such as CD63. This luciferase-based method makes it possible to measure exosomes secreted into the culture medium with high linearity and wide dynamic range in a high-throughput manner. We demonstrate that data obtained by luminescent quantification are well correlated with data obtained by conventional nanoparticle tracking analysis under multiple conditions. In addition, our system is capable of evaluating the recipient cells or tissues that take up exosomes, as well as visualizing exosomes in vivo. The proposed system represents a powerful tool for understanding the molecular mechanisms underlying exosome production, uptake, and long-term distribution.
The apparent activation energy and pre-exponential kinetic factor for heterogeneous calcium carbonate nucleation on quartz
Authors: Li Qingyun , Jun Young-Shin
Published: September 2018

Nucleation occurs widely in materials synthesis and natural environments. However, in the nucleation rate equation, values for the apparent activation energy (Ea) and the pre-exponential kinetic factor (A) are thus far unknown because real-time nanoscale observations are difficult to perform. Here we experimentally determine Ea and A using heterogeneous calcium carbonate nucleation on quartz as a model system. Nucleation rates are measured with in situ grazing incidence small-angle X-ray scattering and ex situ atomic force microscopy, and the experiments are conducted with a fixed supersaturation of IAP/Ksp(calc)  = 101.65 at 12, 25, and 31 °C. Ea is calculated as 45 ± 7 kJ mol−1, and A is 1012.0 ± 1.1 nuclei μm−2 min−1, or 102.9 ± 1.3 mol m−2 min−1. Increasing the temperature shortens the induction time, but does not change nucleus sizes. These parameter values are critical for predicting and controlling the nucleation of materials.
Binary supramolecular networks of bridged triphenylamines with different substituents and identical scaffolds
Authors: Steiner Christian , Yang Zechao , Gliemann Bettina D. , Meinhardt Ute , Gurrath Martin , Ammon Maximilian , Meyer Bernd , Kivala Milan , Maier Sabine
Published: September 2018

Based on scanning tunneling microscopy experiments combined with density functional theory, we report the formation and the electronic structure of porous binary supramolecular networks on Au(111).
Chemical kinetics in an atmospheric pressure helium plasma containing humidity
Authors: Schröter Sandra , Wijaikhum Apiwat , Gibson Andrew R. , West Andrew , Davies Helen L. , Minesi Nicolas , Dedrick James , Wagenaars Erik , de Oliveira Nelson , Nahon Laurent , Kushner Mark J. , Booth Jean-Paul , Niemi Kari , Gans Timo , O'Connell Deborah
Published: September 2018

Investigating the formation and kinetics of O and OH in a He–H2O plasma jet using absorption spectroscopy and 0D modelling.
The electrochemical properties of Co3O4 as a lithium-ion battery electrode: a first-principles study
Authors: Liu Wei-Wei , Lau Woon-Ming , Zhang Yanning
Published: September 2018

Obvious structure distortions and volume expansions occur for LinCo3O4 with n > 1. The distorted surface structure of Li/Co3O4(110) also reduces the rate capability of Co3O4 anode. The lithiation process of LinCo3O4 follows a two-step process of Co3O4 → CoO → Co.
First-principles study of anion diffusion in lead-free halide double perovskites
Authors: Lan Chunfeng , Zhao Shuai , Luo Jingting , Fan Ping
Published: September 2018

In this work, halide ion diffusion in lead-free halide double perovskites Cs2AgBiX6 (X = Cl, Br), Cs2AgSbCl6 and Cs2AgInCl6 was investigated by first-principles calculations.
Excited state intramolecular proton transfer in julolidine derivatives: an ab initio study
Authors: Budzák Šimon , Jacquemin Denis
Published: September 2018

We have studied, using ab initio tools, a series of fluorescent julolidine derivatives, undergoing Excited State Intramolecular Proton Transfer (ESIPT) and some unexpected substitution effects have been found.
Heat transport in pristine and polycrystalline single-layer hexagonal boron nitride
Authors: Dong Haikuan , Hirvonen Petri , Fan Zheyong , Ala-Nissila Tapio
Published: September 2018

Unusual thermal transport in polycrystalline h-BN prepared by phase field crystal model is revealed by large-scale molecular dynamics simulations.
Tuning the photoreactivity of Z-hexatriene photoswitches by substituents – a non-adiabatic molecular dynamics study
Authors: Tapavicza Enrico , Thompson Travis , Redd Kenneth , Kim Dan
Published: September 2018

To understand how substituents can be used to increase the quantum yield of electrocyclic ring-closing in Z-hexatriene (HT) photoswitches, we study the photodynamics of substituted HT derivatives using non-adiabatic molecular dynamics.
Porous graphene doped with Fe/N/S and incorporating Fe3O4 nanoparticles for efficient oxygen reduction
Authors: Li Yi , Zhou Yazhou , Zhu Chengzhou , Hu Yun Hang , Gao Shuai , Liu Qinqin , Cheng Xiaonong , Zhang Lili , Yang Juan , Lin Yuehe
Published: September 2018

The honeycomb-like structured graphene was used to synthesize a 3D porous graphene doped with Fe/N/S and incorporating Fe3O4 nanoparticles. It showed comparable ORR activity to Pt/C, in alkaline media.
Catalytic and stoichiometric flavanone oxidation mediated by nonheme oxoiron(iv) complexes as flavone synthase mimics: kinetic, mechanistic and computational studies
Authors: Turcas Ramona , Kripli Balázs , Attia Amr A. A. , Lakk-Bogáth Dóra , Speier Gábor , Giorgi Michel , Silaghi-Dumitrescu Radu , Kaizer József
Published: September 2018

Stoichiometric and catalytic oxidation of flavanone by nonheme Fe(iv)O, and their Fe(ii) precursors with m-CPBA, as flavone synthase mimics is investigated.
Tissue and plasma proteomics for early stage cancer detection
Authors: Peng Liyuan , Cantor David I. , Huang Canhua , Wang Kui , Baker Mark S. , Nice Edouard C.
Published: September 2018

The pursuit of novel and effective biomarkers is essential in the struggle against cancer, which is a leading cause of mortality worldwide. Here we discuss the relative advantages and disadvantages of the most frequently used proteomics techniques, concentrating on the latest advances and application of tissue and plasma proteomics for novel cancer biomarker discovery.
Predicting the conductance of strongly correlated molecules: the Kondo effect in perchlorotriphenylmethyl/Au junctions
Authors: Appelt W. H. , Droghetti A. , Chioncel L. , Radonjić M. M. , Muñoz E. , Kirchner S. , Vollhardt D. , Rungger I.
Published: September 2018

We predict the non-equilibrium molecular conductance in the Kondo regime from first principles by combining density functional theory with the renormalized super-perturbation theory.
Magnetization dynamics induced by the Rashba effect in ferromagnetic films
Authors: Yu Zhizhou , Chen Jian , Zhang Lei , Xing Yanxia , Wang Jian
Published: September 2018

Current-induced magnetization dynamics due to spin–orbit torque were studied from the perspective of quantum transport under two different types of Rashba interaction.
Supported lipid bilayers with encapsulated quantum dots (QDs) via liposome fusion: effect of QD size on bilayer formation and structure
Authors: Wlodek Magdalena , Kolasinska-Sojka Marta , Szuwarzynski Michal , Kereïche Sami , Kovacik Lubomir , Zhou Liangzhi , Islas Luisa , Warszynski Piotr , Briscoe Wuge H.
Published: September 2018

The formation kinetics and structure of supported lipid bilayers embedded with quantum-dots (QDs) depend on the QD size.
Exciton and phonon dynamics in highly aligned 7-atom wide armchair graphene nanoribbons as seen by time-resolved spontaneous Raman scattering
Authors: Zhu Jingyi , German Raphael , Senkovskiy Boris V. , Haberer Danny , Fischer Felix R. , Grüneis Alexander , van Loosdrecht Paul H. M.
Published: September 2018

Time-resolved spontaneous Raman experiments on 7-AGNRs show the presence of a long lived excitonic dark state together with short and long lived trap states.
Rhodium(iii)-catalyzed three-component cascade synthesis of 6H-benzo[c]chromenes through C–H activation
Authors: Yang Wei , Wang Jingyi , Wang He , Li Lei , Guan Yuekai , Xu Xianxiu , Yu Dayu
Published: September 2018

An efficient procedure for 6H-benzo[c]chromenes via a new Rh(iii)-catalyzed domino annulation is described.
Light-driven exchange between extended and contracted lasso-like isomers of a bistable [1]rotaxane
Authors: Saura-Sanmartin Adrian , Martinez-Cuezva Alberto , Pastor Aurelia , Bautista Delia , Berna Jose
Published: September 2018

A photoactive hydrogen-bonded lasso having an amide-based [1]rotaxane structure has been constructed from acyclic precursors through a self-templating approach. The stability, structural integrity and switching are described.
Ru(ii)-Catalyzed C6-selective C–H amidation of 2-pyridones
Authors: Zhang Lei , Zheng Xiangyun , Chen Jinkang , Cheng Kang , Jin Licheng , Jiang Xinpeng , Yu Chuanming
Published: September 2018

An efficient Ru-catalyzed C6 site-selective amidation of 2-pyridones has been accomplished with dioxazolone under mild conditions.
Construction of 3D architectures with Ni(HCO3)2 nanocubes wrapped by reduced graphene oxide for LIBs: ultrahigh capacity, ultrafast rate capability and ultralong cycle stability
Authors: Dong Yutao , Ma Yuhang , Li Dan , Liu Yushan , Chen Weihua , Feng Xiangming , Zhang Jianmin
Published: September 2018

A 3D layered Ni(HCO3)2/rGO nano-architecture was fabricated by coordination self-assembly for high performance storage of Li-ions with fast electrode kinetics and a super-long life.
Laser trapping/confocal Raman spectroscopic characterization of PLGA-PEG nanoparticles
Authors: Yang Jie , Zhang Ruo-Nan , Liu Dong-Jie , Zhou Xu , Shoji Tatsuya , Tsuboi Yasuyuki , Yan Hu
Published: September 2018

We have immobilized poly(ethylene glycol) (PEG) on the surfaces of poly(lactic-co-glycolic acid) (PLGA) nanoparticles by two different chemical methods, i.e., SOCl2 halogenate-alcoholysis and DCC dehydration. The PEG-immobilized PLGA nanoparticles were precisely characterized by the laser trapping/confocal Raman spectroscope.
Activity and selectivity regulation through varying the size of cobalt active sites in photocatalytic CO2 reduction
Authors: Mu Qiaoqiao , Zhu Wei , Yan Gangbin , Lian Yuebin , Yao Yuanzhou , Li Qin , Tian Yuyu , Zhang Peng , Deng Zhao , Peng Yang
Published: September 2018

The development of efficient and economical catalysts for photocatalytic reduction of CO2 into chemical feedstocks is highly desirable for addressing both the global energy crisis and carbon emission problem.
Porous and high-strength graphitic carbon/SiC three-dimensional electrode for capacitive deionization and fuel cell applications
Authors: Xue Yifei , Xie Jiangzhou , He Meng , Liu Mingquan , Xu Min , Ni Wei , Yan Yi-Ming
Published: September 2018

A high-strength macroscale silicon carbide reinforced carbon-based 3D conductive framework was fabricated for capacitive deionization and fuel cell applications.
Selective photocatalytic benzene hydroxylation to phenol using surface-modified Cu2O supported on graphene
Authors: He Jinbao , Zhang Min , Primo Ana , García Hermenegildo , Li Zhaohui
Published: September 2018

The photocatalytic activity for benzene hydroxylation to phenol by hydrogen peroxide has been evaluated using a series of photocatalysts based on defective graphene.
Engineering heteroatoms with atomic precision in donor–acceptor covalent triazine frameworks to boost photocatalytic hydrogen production
Authors: Guo Liping , Niu Yingli , Xu Haitao , Li Qingwei , Razzaque Shumaila , Huang Qi , Jin Shangbin , Tan Bien
Published: September 2018

Engineering heteroatoms that precisely positioned in covalent triazine frameworks (CTFs) can dramatically enhance the photocatalytic hydrogen evolution rate of CTFs and is thus an effective strategy to improve the photocatalysis performance for porous organic polymers (POPs).
Correction: Improving the exciton dissociation of polymer/fullerene interfaces with a minimal loading amount of energy cascading molecular dopant
Authors: Wang Yang , Xu Weidong , Yi Jianpeng , Zuo Chao , Gong Yanting , Liu Yuanyuan , Lai Wen-Yong , Huang Wei
Published: September 2018

Correction for ‘Improving the exciton dissociation of polymer/fullerene interfaces with a minimal loading amount of energy cascading molecular dopant’ by Yang Wang et al., J. Mater. Chem. A, 2018, 6, 15977–15984.
The great escape: how cationic polyplexes overcome the endosomal barrier
Authors: Bus Tanja , Traeger Anja , Schubert Ulrich S.
Published: September 2018

Endo-lysosomal escape strategies of cationic polymer-mediated gene delivery at a glance.
A2–A1–D–A1–A2 type non-fullerene acceptors based on methoxy substituted benzotriazole with three different end-capped groups for P3HT-based organic solar cells
Authors: Zhang Qianqian , Xiao Bo , Du Mengzhen , Li Gongqiang , Tang Ailing , Zhou Erjun
Published: September 2018

In the last three years, the A2–A1–D–A1–A2 skeleton has become increasingly popular in the design of non-fullerene acceptors (NFAs), and it could match particularly well with the classic p-type polymer of poly(3-hexylthiophene) (P3HT).
Reduced‐order non‐linear generalised minimum variance control for quasi‐linear parameter varying systems
Authors: Grimble Mike J.
Published: September 2018

A reduced‐order non‐linear generalised minimum variance (NGMV) controller is introduced. The NGMV controller is one of the simplest control solutions for non‐linear systems, with flexibility regarding the form of the non‐linear system and the type of cost‐function that may include non‐linear elements. The new element is to introduce a pre‐specified low‐order controller structure. The motivation was the need to develop a non‐linear industrial controller that has a simple structure and is easy to understand. The optimisation problem is to generate the optimal feedback controller gains or controller parameters on‐line. These computations involve background processing to optimise gains or parameters. The gains vary as setpoints or disturbances change but for much of the time these are approximately constant. The approach provides a model‐based optimal control solution, but in a form where classically trained engineers can easily retune if needed.