bluuebunny/crossref_metadata_2025 huggingface dataset:
Non-invasive detection of language-related prefrontal high gamma band activity with beamforming MEG
Authors: Hashimoto Hiroaki , Hasegawa Yuka , Araki Toshihiko , Sugata Hisato , Yanagisawa Takufumi , Yorifuji Shiro , Hirata Masayuki
Published: October 2017

High gamma band (>50 Hz) activity is a key oscillatory phenomenon of brain activation. However, there has not been a non-invasive method established to detect language-related high gamma band activity. We used a 160-channel whole-head magnetoencephalography (MEG) system equipped with superconducting quantum interference device (SQUID) gradiometers to non-invasively investigate neuromagnetic activities during silent reading and verb generation tasks in 15 healthy participants. Individual data were divided into alpha (8–13 Hz), beta (13–25 Hz), low gamma (25–50 Hz), and high gamma (50–100 Hz) bands and analysed with the beamformer method. The time window was consecutively moved. Group analysis was performed to delineate common areas of brain activation. In the verb generation task, transient power increases in the high gamma band appeared in the left middle frontal gyrus (MFG) at the 550–750 ms post-stimulus window. We set a virtual sensor on the left MFG for time-frequency analysis, and high gamma event-related synchronization (ERS) induced by a verb generation task was demonstrated at 650 ms. In contrast, ERS in the high gamma band was not detected in the silent reading task. Thus, our study successfully non-invasively measured language-related prefrontal high gamma band activity.
An absorption-free and Doppler-improved optical waveguide for diffractionless light propagation
Authors: Cui Ni , Gan Ziyang , Zhang Lida
Published: October 2017

We propose a novel scheme to realize an optical waveguide induced by an active Raman gain (ARG) process in a four-level N-type atomic system. Because of the nature of the ARG, there are two distinct features related to the waveguide: i) It is not absorptive, on the contrary, weak gain is presented; ii) It can be improved by the Doppler effect in the sense that the dispersion is enhanced while the gain is further reduced. This is in sharp contrast to the previously considered schemes where usually the optical induced waveguide is passive and is severely attenuated by the Doppler effect. We then study the paraxial light propagation in the waveguide which shows that the propagation dynamics is lossless and diffractionless.
Monitoring ground water storage at mesoscale using seismic noise: 30 years of continuous observation and thermo-elastic and hydrological modeling
Authors: Lecocq Thomas , Longuevergne Laurent , Pedersen Helle Anette , Brenguier Florent , Stammler Klaus
Published: October 2017

Groundwater is a vital freshwater resource for both humans and ecosystems. Achieving sustainable management requires a detailed knowledge of the aquifer structure and of its behavior in response to climatic and anthropogenic forcing. Traditional monitoring is carried out using piezometer networks, and recently complemented with new geophysical or satellite-based observations. These techniques survey either local (small-scale) water systems or regional areas (large scale) but, to date, adequate observation tools are lacking at the water management scale (i.e. several tens of kms), which is generally explored by modeling. Using 30 years of continuous recording by four seismic stations of the Gräfenberg Array (Germany), we demonstrate that long-term observations of velocity variations (approximately 0.01%) of surface waves can be extracted from such recordings of ocean-generated seismic noise. These small variations can be explained by changes to mechanical properties of the complex aquifer system in the top few hundred meters of the crust. The velocity changes can be interpreted as effects of temperature diffusion and water storage changes. Seismic noise recordings may become a new and valuable tool to monitor heterogeneous groundwater systems at mesoscale, in addition to existing observation methods.
Nanog-driven cell-reprogramming and self-renewal maintenance in Ptch1
+/− granule cell precursors after radiation injury
Authors: Tanno Barbara , Leonardi Simona , Babini Gabriele , Giardullo Paola , De Stefano Ilaria , Pasquali Emanuela , Saran Anna , Mancuso Mariateresa
Published: October 2017

Medulloblastoma (MB) is the most common pediatric brain tumor, comprising four distinct molecular variants, one of which characterized by activation of the Sonic Hedgehog (SHH) pathway, driving 25–30% of sporadic MB. SHH-dependent MBs arise from granule cell precursors (GCPs), are fatal in 40–70% of cases and radioresistance strongly contributes to poor prognosis and tumor recurrence. Patched1 heterozygous (Ptch1+/−) mice, carrying a germ-line heterozygous inactivating mutation in the Ptch1 gene, the Shh receptor and negative regulator of the pathway, are uniquely susceptible to MB development after radiation damage in neonatal cerebellum. Here, we irradiated ex-vivo GCPs isolated from cerebella of neonatal WT and Ptch1+/− mice. Our results highlight a less differentiated status of Ptch1-mutated cells after irradiation, influencing DNA damage response. Increased expression levels of pluripotency genes Nanog, Oct4 and Sal4, together with greater clonogenic potential, clearly suggest that radiation induces expansion of the stem-like cell compartment through cell-reprogramming and self-renewal maintenance, and that this mechanism is strongly dependent on Nanog. These results contribute to clarify the molecular mechanisms that control radiation-induced Shh-mediated tumorigenesis and may suggest Nanog as a potential target to inhibit for adjuvant radiotherapy in treatment of SHH-dependent MB.
Acceleration of a trailing positron bunch in a plasma wakefield accelerator
Authors: Doche A. , Beekman C. , Corde S. , Allen J. M. , Clarke C. I. , Frederico J. , Gessner S. J. , Green S. Z. , Hogan M. J. , O’Shea B. , Yakimenko V. , An W. , Clayton C. E. , Joshi C. , Marsh K. A. , Mori W. B. , Vafaei-Najafabadi N. , Litos M. D. , Adli E. , Lindstrøm C. A. , Lu W.
Published: October 2017

High gradients of energy gain and high energy efficiency are necessary parameters for compact, cost-efficient and high-energy particle colliders. Plasma Wakefield Accelerators (PWFA) offer both, making them attractive candidates for next-generation colliders. In these devices, a charge-density plasma wave is excited by an ultra-relativistic bunch of charged particles (the drive bunch). The energy in the wave can be extracted by a second bunch (the trailing bunch), as this bunch propagates in the wake of the drive bunch. While a trailing electron bunch was accelerated in a plasma with more than a gigaelectronvolt of energy gain, accelerating a trailing positron bunch in a plasma is much more challenging as the plasma response can be asymmetric for positrons and electrons. We report the demonstration of the energy gain by a distinct trailing positron bunch in a plasma wakefield accelerator, spanning nonlinear to quasi-linear regimes, and unveil the beam loading process underlying the accelerator energy efficiency. A positron bunch is used to drive the plasma wake in the experiment, though the quasi-linear wake structure could as easily be formed by an electron bunch or a laser driver. The results thus mark the first acceleration of a distinct positron bunch in plasma-based particle accelerators.
Plasmonically Enhanced Schottky Photovoltaic Devices
Authors: Farhat M. , Kais S. , Alharbi F. H.
Published: October 2017

Solar-cells based on Schottky junctions between metals and semiconductors (without or with an intermediate insulator) are among the main possibilities towards economical photovoltaic conversion of the solar energy. This is mainly due to their structural simplicity and hence the ease of their realization. We propose here a new kind of light-harvesting devices using plasmonic nano-antenna gratings, that enhance the absorption of light over a broadband spectrum, and permit the reduction of thickness of the cell dramatically, with efficiency around 15% for 3 micrometers ultra-thin Silicon cell. We show that this technique may provide a new avenue in low cost fabrication of thin-film solar-cells.
Chemical and kinetic insights into the Thermal Decomposition of an Oxide Layer on Si(111) from Millisecond Photoelectron Spectroscopy
Authors: Gallet J.-J. , Silly M. G. , Kazzi M. El , Bournel F. , Sirotti F. , Rochet F.
Published: October 2017

Despite thermal silicon oxide desorption is a basic operation in semiconductor nanotechnology, its detailed chemical analysis has not been yet realized via time-resolved photoemission. Using an advanced acquisition system and synchrotron radiation, heating schedules with velocities as high as 100 K.s−1 were implemented and highly resolved Si 2p spectra in the tens of millisecond range were obtained. Starting from a Si(111)-7 × 7 surface oxidized in O2 at room temperature (1.4 monolayer of oxygen), changes in the Si 2p spectral shape enabled a detailed chemical analysis of the oxygen redistribution at the surface and of the nucleation, growth and reconstruction of the clean silicon areas. As desorption is an inhomogeneous surface process, the Avrami formalism was adapted to oxide desorption via an original mathematical analysis. The extracted kinetic parameters (the Avrami exponent equal to ~2, the activation energy of ~4.1 eV and a characteristic frequency) were found remarkably stable within a wide (~110 K) desorption temperature window, showing that the Avrami analysis is robust. Both the chemical and kinetic information collected from this experiment can find useful applications when desorption of the oxide layer is a fundamental step in nanofabrication processes on silicon surfaces.
Zebra rocks: compaction waves create ore deposits
Authors: Kelka Ulrich , Veveakis Manolis , Koehn Daniel , Beaudoin Nicolas
Published: October 2017

Nature has a range of distinct mechanisms that cause initially heterogeneous systems to break their symmetry and form patterns. One of these patterns is zebra dolomite that is frequently hosting economically important base metal mineralization. A consistent generic model for the genesis of these periodically banded rocks is still lacking. In this contribution, we present for the first time a fully consistent mathematical model for the genesis of the pattern by coupling the reactive fluid-solid system with hydromechanics. We show that visual banding develops at a given stress and host-rock permeability indicating that the wavelength and occurrence of the pattern may be predictable for natural settings. This finding offers the exciting possibility of estimating conditions of formation of known deposits as well as forecasting potential exploration targets.
The avian egg exhibits general allometric invariances in mechanical design
Authors: Juang Jia-Yang , Chen Pin-Yi , Yang Da-Chang , Wu Shang-Ping , Yen An , Hsieh Hsin-I.
Published: October 2017

The avian egg exhibits extraordinary diversity in size, shape and color, and has a key role in avian adaptive radiations. Despite extensive work, our understanding of the underlying principles that guide the “design” of the egg as a load-bearing structure remains incomplete, especially over broad taxonomic scales. Here we define a dimensionless number C, a function of egg weight, stiffness and dimensions, to quantify how stiff an egg is with respect to its weight after removing geometry-induced rigidity. We analyze eggs of 463 bird species in 36 orders across five orders of magnitude in body mass, and find that C number is nearly invariant for most species, including tiny hummingbirds and giant elephant birds. This invariance or “design guideline” dictates that evolutionary changes in shell thickness and Young’s modulus, both contributing to shell stiffness, are constrained by changes in egg weight. Our analysis illuminates unique reproductive strategies of brood parasites, kiwis, and megapodes, and quantifies the loss of safety margin for contact incubation due to artificial selection and environmental toxins. Our approach provides a mechanistic framework for a better understanding of the mechanical design of the avian egg, and may provide clues to the evolutionary origin of contact incubation of amniote eggs.
Comprehensive Real-Time Analysis of the Yeast Volatilome
Authors: Tejero Rioseras Alberto , Garcia Gomez Diego , Ebert Birgitta E. , Blank Lars M. , Ibáñez Alfredo J. , Sinues Pablo M-L
Published: October 2017

While yeast is one of the most studied organisms, its intricate biology remains to be fully mapped and understood. This is especially the case when it comes to capture rapid, in vivo fluctuations of metabolite levels. Secondary electrospray ionization-high resolution mass spectrometry SESI-HRMS is introduced here as a sensitive and noninvasive analytical technique for online monitoring of microbial metabolic activity. The power of this technique is exemplarily shown for baker’s yeast fermentation, for which the time-resolved abundance of about 300 metabolites is demonstrated. The results suggest that a large number of metabolites produced by yeast from glucose neither are reported in the literature nor are their biochemical origins deciphered. With the technique demonstrated here, researchers interested in distant disciplines such as yeast physiology and food quality will gain new insights into the biochemical capability of this simple eukaryote.
Occipital GABA levels in older adults and their relationship to visual perceptual suppression
Authors: Pitchaimuthu Kabilan , Wu Qi-zhu , Carter Olivia , Nguyen Bao N. , Ahn Sinyeob , Egan Gary F. , McKendrick Allison M.
Published: October 2017

Several studies have attributed certain visual perceptual alterations in older adults to a likely decrease in GABA (Gamma Aminobutyric Acid) concentration in visual cortex, an assumption based on findings in aged non-human primates. However, to our knowledge, there is no direct evidence for an age-related decrease in GABA concentration in human visual cortex. Here, we estimated visual cortical GABA levels and Glx (combined estimate of glutamate and glutamine) levels using magnetic resonance spectroscopy. We also measured performance for two visual tasks that are hypothesised to be mediated, at least in part, by GABAergic inhibition: spatial suppression of motion and binocular rivalry. Our results show increased visual cortical GABA levels, and reduced Glx levels, in older adults. Perceptual performance differed between younger and older groups for both tasks. When subjects of all ages were combined, visual cortical GABA levels but not Glx levels correlated with perceptual performance. No relationship was found between perception and GABA levels in dorsolateral prefrontal cortex. Perceptual measures and GABA were not correlated when either age group was considered separately. Our results challenge current assumptions regarding neurobiological changes that occur within the aging human visual cortex and their association with certain age-related changes in visual perception.
Olfactory detection of a bacterial short-chain fatty acid acts as an orexigenic signal in Drosophila melanogaster larvae
Authors: Depetris-Chauvin Ana , Galagovsky Diego , Chevalier Charlene , Maniere Gerard , Grosjean Yael
Published: October 2017

Microorganisms inhabiting fermenting fruit produce chemicals that elicit strong behavioral responses in flies. Depending on their ecological niche, individuals confer a positive or a negative valence to a chemical and, accordingly, they trigger either attractive or repulsive behaviors. We studied the case of bacterial short-chain fatty acids (SCFA) that trigger opposite behaviors in adult and larvae of Drosophila melanogaster. We determined that SCFA-attractive responses depend on two larval exclusive chemoreceptors, Or30a and Or94b. Of those SCFA, propionic acid improves larval survival in suboptimal rearing conditions and supports growth. Olfactory detection of propionic acid specifically is sufficient to trigger feeding behaviors, and this effect requires the correct activity of Or30a+ and Or94b+ olfactory sensory neurons. Additionally, we studied the case of the invasive pest Drosophila suzukii that lives on undamaged ripe fruit with less SCFA production. Contrary to D. melanogaster, D. suzukii larvae show reduced attraction towards propionic acid, which does not trigger feeding behavior in this invasive species. Our results demonstrate the relevance of propionic acid as an orexigenic signal in D. melanogaster larvae. Moreover, this study underlines that the changes on ecological niche are accompanied with alterations of olfactory preferences and vital olfactory driven behaviors.
Transformation from Film to Nanorod via a Sacrifical Layer: Pulsed Laser Deposition of ZnO for Enhancing Photodetector Performance
Authors: Ou Sin-Liang , Yu Fei-Peng , Wuu Dong-Sing
Published: October 2017

A novel fabrication method for single crystalline ZnO nanorods by pulsed laser deposition (PLD) using a chemical-bath-deposited ZnS seed layer is proposed. For the substrate temperature (Ts) lower than 700 °C, the PLD-ZnO showed a polycrystalline phase and film-type morphology, resulting from the ZnS seed layer with a cubic phase. However, the ZnS film became a sacrifical layer and single crystalline ZnO(002) nanorods can be achieved at Ts of 900 °C, where ZnS was decomposed to zinc metals and sulfur fumes. The transformation from ZnO film to nanorod microstructure was demonstrated with the change of ZnS layer into Zn grains. Enhanced performance of the metal-semiconductor-metal photodetectors were fabricated with ZnO/ZnS samples grown at Ts of 500, 700, and 900 °C. The responsivities (@1 V and 370 nm) of these three devices were 1.71, 6.35, and 98.67 A/W, while their UV-to-visible discrimination ratios were 7.2, 16.5, and 439.1, respectively. Obviously, a higher light-capturing efficiency was obtained in the 900 °C-grown ZnO/ZnS device owing to its one-dimensional nanostructure with high crystal quality. The results indicate PLD combined with a sacrifical nanostructure is a promising method for obtaining high-quality ZnO nanorods, which paves the way for the fabrication of high performance ZnO-based devices.
UClncR: Ultrafast and comprehensive long non-coding RNA detection from RNA-seq
Authors: Sun Zhifu , Nair Asha , Chen Xianfeng , Prodduturi Naresh , Wang Junwen , Kocher Jean-Pierre
Published: October 2017

Long non-coding RNA (lncRNA) is a large class of gene transcripts with regulatory functions discovered in recent years. Many more are expected to be revealed with accumulation of RNA-seq data from diverse types of normal and diseased tissues. However, discovering novel lncRNAs and accurately quantifying known lncRNAs is not trivial from massive RNA-seq data. Herein we describe UClncR, an Ultrafast and Comprehensive lncRNA detection pipeline to tackle the challenge. UClncR takes standard RNA-seq alignment file, performs transcript assembly, predicts lncRNA candidates, quantifies and annotates both known and novel lncRNA candidates, and generates a convenient report for downstream analysis. The pipeline accommodates both un-stranded and stranded RNA-seq so that lncRNAs overlapping with other genes can be predicted and quantified. UClncR is fully parallelized in a cluster environment yet allows users to run samples sequentially without a cluster. The pipeline can process a typical RNA-seq sample in a matter of minutes and complete hundreds of samples in a matter of hours. Analysis of predicted lncRNAs from two test datasets demonstrated UClncR’s accuracy and their relevance to sample clinical phenotypes. UClncR would facilitate researchers’ novel lncRNA discovery significantly and is publically available at http://bioinformaticstools.mayo.edu/research/UClncR.
A missense mutation in SLC26A3 is associated with human male subfertility and impaired activation of CFTR
Authors: Wedenoja Satu , Khamaysi Ahlam , Shimshilashvili Liana , Anbtawe-Jomaa Shireen , Elomaa Outi , Toppari Jorma , Höglund Pia , Aittomäki Kristiina , Holmberg Christer , Hovatta Outi , Tapanainen Juha S. , Ohana Ehud , Kere Juha
Published: October 2017

Chloride absorption and bicarbonate excretion through exchange by the solute carrier family 26 member 3 (SLC26A3) and cystic fibrosis transmembrane conductance regulator (CFTR) are crucial for many tissues including sperm and epithelia of the male reproductive tract. HomozygousSLC26A3mutations cause congenital chloride diarrhea with male subfertility, while homozygousCFTRmutations cause cystic fibrosis with male infertility. Some homozygous or heterozygousCFTRmutations only manifest as male infertility. Accordingly, we studied the influence ofSLC26A3on idiopathic infertility by sequencing exons ofSLC26A3in 283 infertile and 211 control men. A heterozygous mutation c.2062 G > C (p.Asp688His) appeared in nine (3.2%) infertile men, and additionally, in two (0.9%) control men, whose samples revealed a sperm motility defect. The p.Asp688His mutation is localized in the CFTR-interacting STAS domain of SLC26A3 and enriched in Finland, showing a significant association with male infertility in comparison with 6,572 Finnish (P < 0.05) and over 120,000 global alleles (P < 0.0001) (ExAC database). Functional studies showed that while SLC26A3 is a strong activator of CFTR-dependent anion transport, SLC26A3-p.Asp688His mutant retains normal Cl−/HCO3−exchange activity but suppresses CFTR, despite unaffected domain binding and expression. These results suggest a novel mechanism for human male infertility─impaired anion transport by the coupled SLC26A3 and CFTR.
Embodiment in a virtual body that speaks produces agency over the speaking but does not necessarily influence subsequent real speaking
Authors: Banakou Domna , Slater Mel
Published: October 2017

Previous results have shown that body ownership, induced through first-person perspective (1PP) over a virtual body (VB) that moves synchronously with real body movements, can lead to illusory agency over VB utterances even though the participant does not speak. It was also found that when participants later speak they follow the fundamental frequency (FF) of the voice of their VB, indicating a new motor plan for speaking. To eliminate the contribution of veridical agency over the VB movements, we conducted a study where we induced body ownership using visuotactile (VT) synchrony rather than visuomotor. Participants saw a life-sized VB from 1PP and reflected in a virtual mirror, that spoke with corresponding lip movements. Half of the 36 experimental participants experienced synchronous (Sync) passive VT on their hands and abdomen, and the other half asynchronous (Async). We found that both VT Sync and Async conditions resulted in a strong subjective illusion of body ownership and agency over the VB, but not, however, changes in voice FF in subsequent speaking. This shows that although illusory agency may be associated with body ownership, a change in motor plan is likely to be a generalisation from veridical agency over whole body movements.
SFRP4 gene expression is increased in aggressive prostate cancer
Authors: Sandsmark Elise , Andersen Maria K. , Bofin Anna M. , Bertilsson Helena , Drabløs Finn , Bathen Tone F. , Rye Morten B. , Tessem May-Britt
Published: October 2017

Increased knowledge of the molecular differences between indolent and aggressive prostate cancer is needed for improved risk stratification and treatment selection. Secreted frizzled-related protein 4 (SFRP4) is a modulator of the cancer-associated Wnt pathway, and previously suggested as a potential marker for prostate cancer aggressiveness. In this study, we investigated and validated the association between SFRP4 gene expression and aggressiveness in nine independent cohorts (n = 2157). By differential expression and combined meta-analysis of all cohorts, we detected significantly higher SFRP4 expression in cancer compared with normal samples, and in high (3–5) compared with low (1–2) Grade Group samples. SFRP4 expression was a significant predictor of biochemical recurrence in six of seven cohorts and in the overall analysis, and was a significant predictor of metastatic event in one cohort. In our study cohort, where metabolic information was available, SFRP4 expression correlated significantly with the concentrations of citrate and spermine, two previously suggested biomarkers for aggressive prostate cancer. SFRP4 immunohistochemistry in an independent cohort (n = 33) was not associated with aggressiveness. To conclude, high SFRP4 gene expression is associated with high Grade Group and recurrent prostate cancer after surgery. Future studies investigating the mechanistic and clinical usefulness of SFRP4 in prostate cancer are warranted.
Hemoglobin variants shape the distribution of malaria parasites in human populations and their transmission potential
Authors: Gonçalves Bronner P. , Sagara Issaka , Coulibaly Mamadou , Wu Yimin , Assadou Mahamadoun H. , Guindo Agnes , Ellis Ruth D. , Diakite Mahamadou , Gabriel Erin , Prevots D. Rebecca , Doumbo Ogobara K. , Duffy Patrick E.
Published: October 2017

Hemoglobin variants C and S protect against severe malaria but their influence on parameters not directly linked to disease severity such as gametocyte carriage and infection chronicity is less well understood. To assess whether these infection-related phenotypes depend on the host hemoglobin genotype, we followed 500 Malian individuals over 1–2 years and determined their parasitological status during monthly visits and incidental clinical episodes. While adults heterozygous for hemoglobin S mutation were less often parasitemic compared to AA adults (odds ratio [OR] 0.50 95% confidence interval [CI] 0.31–0.79, P = 0.003), schoolchildren (but not toddlers or adults) with AC genotype carried parasites, including gametocytes, more often than their AA counterparts (OR 3.01 95% CI 1.38–6.57, P = 0.006). AC children were also likelier to be parasite-positive during the dry season, suggesting longer infections, and were more infectious in mosquito skin feeding assays than AA children. Notably, AC school-aged children, who comprise ~5% of the population, harbor a third of infections with patent gametocytes between May and August, when transmission transitions from very low to intense. These findings indicate that schoolchildren with hemoglobin C mutation might contribute disproportionately to the seasonal malaria resurgence in parts of West Africa where the HbC variant is common.
Electronic Cigarette Smoke Impairs Normal Mesenchymal Stem Cell Differentiation
Authors: Shaito A. , Saliba J. , Husari A. , El-Harakeh M. , Chhouri H. , Hashem Y. , Shihadeh A. , El-Sabban M.
Published: October 2017

Electronic cigarettes (e-cigarettes) are promoted as low-risk alternatives to combustible cigarettes. However, the effects of chronic inhalation of potential toxicants emitted by ecigarettes remain largely unexamined. It is conceivable that smoking-induced chronic diseases result in cellular injury, in the absence of effective repair by stem cells. This study evaluates the effect of cigarette and e-cigarette aerosol extracts on the survival and differentiation of bone marrow-derived mesenchymal stem cells (MSCs). MSC growth and osteogenic differentiation were examined after exposure to smoke extracts. Data revealed detrimental effects of both cigarette and e-cigarette extracts on MSC morphology and growth. Levels and activity of alkaline phosphatase, an osteogenic marker, decreased and induction of osteoblastic differentiation was impaired. Both smoke extracts prevented osteogenic differentiation from progressing, evident by decreased expression of terminal osteogenic markers and mineralization. Elevated levels of reactive oxygen species (ROS) were detected in cells exposed to smoke extracts. Moreover, decreased differentiation potential was concomitant with severe down-regulation of Connexin 43 expression, leading to the loss of gap junction-mediated communication, which together with elevated ROS levels, could explain decreased proliferation and loss of differentiation potential. Hence, e-cigarettes present similar risk as combustible cigarettes with respect to tissue repair impairment.
Yeast diversity in relation to the production of fuels and chemicals
Authors: Wu Jia , Elliston Adam , Le Gall Gwenaelle , Colquhoun Ian J. , Collins Samuel R. A. , Dicks Jo , Roberts Ian N. , Waldron Keith W.
Published: October 2017

In addition to ethanol, yeasts have the potential to produce many other industrially-relevant chemicals from numerous different carbon sources. However there remains a paucity of information about overall capability across the yeast family tree. Here, 11 diverse species of yeasts with genetic backgrounds representative of different branches of the family tree were investigated. They were compared for their abilities to grow on a range of sugar carbon sources, to produce potential platform chemicals from such substrates and to ferment hydrothermally pretreated rice straw under simultaneous saccharification and fermentation conditions. The yeasts differed considerably in their metabolic capabilities and production of ethanol. A number could produce significant amounts of ethyl acetate, arabinitol, glycerol and acetate in addition to ethanol, including from hitherto unreported carbon sources. They also demonstrated widely differing efficiencies in the fermentation of sugars derived from pre-treated rice straw biomass and differential sensitivities to fermentation inhibitors. A new catabolic property of Rhodotorula mucilaginosa (NCYC 65) was discovered in which sugar substrate is cleaved but the products are not metabolised. We propose that engineering this and some of the other properties discovered in this study and transferring such properties to conventional industrial yeast strains could greatly expand their biotechnological utility.
A Hybrid Gate Dielectrics of Ion Gel with Ultra-Thin Passivation Layer for High-Performance Transistors Based on Two-Dimensional Semiconductor Channels
Authors: Jo Hyunjin , Choi Jeong-Hun , Hyun Cheol-Min , Seo Seung-Young , Kim Da Young , Kim Chang-Min , Lee Myoung-Jae , Kwon Jung-Dae , Moon Hyoung-Seok , Kwon Se-Hun , Ahn Ji-Hoon
Published: October 2017

We propose a hybrid gate structure for ion gel dielectrics using an ultra-thin Al2O3 passivation layer for realizing high-performance devices based on electric-double-layer capacitors. Electric-double-layer transistors can be applied to practical devices with flexibility and transparency as well as research on the fundamental physical properties of channel materials; however, they suffer from inherent unwanted leakage currents between electrodes, especially for channel materials with low off-currents. Therefore, the Al2O3 passivation layer was introduced between the metal electrodes and ion gel film as a leakage current barrier; this simple approach effectively reduced the leakage current without capacitance degradation. In addition, we confirmed that a monolayer MoS2 transistor fabricated with the proposed hybrid gate dielectric exhibited remarkably enhanced device properties compared to a transistor using a normal ion gel gate dielectric. Our findings on a simple method to improve the leakage current properties of ion gels could be applied extensively to realize high-performance electric-double-layer transistors utilizing various channel materials.
The role of Thyroid Transcription Factor-1 and Tumor differentiation in Resected Lung Adenocarcinoma
Authors: Huang Tsai-Wang , Lin Ke- Feng , Lee Chien-Hsing , Chang Hung , Lee Shih-Chun , Shieh Yi-Shing
Published: October 2017

To investigate the role of thyroid transcription factor-1 (TTF-1) and tumor differentiation in resected lung adenocarcinoma. A total of 520 patients with clinical early stage lung adenocarcinoma who underwent surgical resection were reviewed retrospectively. Clinical data and outcomes were evaluated with an average follow-up of 117 months. The results were validated via lung cancer cell line studies. The clinical parameters did not differ between relapse and nonrelapse patients. Exceptions were tumor differentiation, lymphovascular space invasion, F18-fluorodeoxyglucose maximum standard uptake value, tumor size, and pathological stage (p < 0.001). Poor tumor differentiation was the independent prognostic factor (odds ratio: 2.937,p = 0.026). The expression of TTF-1 was correlated with tumor differentiation in resected lung adenocarcinoma patients (p < 0.001). Five-year survival was 60.0% for score 1 TTF-1 expression patients, 80.1% for score 2 TTF-1 expression patients, and 86.1% for score 3 TTF-1 expression group patients. The lung cancer cell line study of knockdown and overexpression of TTF-1 revealed TTF-1 mediated High Mobility Group AT-Hook 2 (HMGA2) protein involved with epithelium-mesenchymal transformation. The chromatin immunoprecipitation revealed TTF-1 regulated HMGA2 via direct binding. TTF-1/HMGA2 axis was associated with tumor differentiation and mediated the aggressiveness of the tumor and prognosis.
Development of a Curative Therapeutic Vaccine (TheraVac) for the Treatment of Large Established Tumors
Authors: Nie Yingjie , Yang De , Trivett Anna , Han Zhen , Xin Haiyun , Chen Xin , Oppenheim Joost J.
Published: October 2017

Harnessing immune system to treat cancer requires simultaneous generation of tumor-specific CTLs and curtailment of tumor immunosuppressive environment. Here, we developed an immunotherapeutic regimen capable of eliminating large established mouse tumors using HMGN1, a DC-activating TLR4 agonist capable of inducing anti-tumor immunity. Intratumoral delivery of HMGN1 with low dose of Cytoxan cured mice bearing small (∅ ≈ 0.5 cm), but not large (∅ ≈ 1.0 cm) CT26 tumors. Screening for activators capable of synergizing with HMGN1 in activating DC identified R848. Intratumoral delivery of HMGN1 and R848 plus Cytoxan eradicated large established CT26 tumors. The resultant tumor-free mice were resistant to subsequent challenge with CT26, indicating the generation of CT26-specific protective immunity. This immunotherapeutic regimen caused homing of tumor-infiltrating DC to draining lymph nodes and increased infiltration of T cells into tumor tissues. Cytoxan in this regimen could be replaced by anti-CTLA4) or anti-PD-L1. Importantly, this immunotherapeutic regimen was also curative for large established mouse Renca and EG7 tumors. Thus, we have developed a curative therapeutic vaccination regimen dubbed ‘TheraVac’ consisting of HMGN1 and R848 plus a checkpoint inhibitor, that can, without using exogenous tumor-associated antigen(s), eliminate various large tumors and induce tumor-specific immunity.
High potential thermoelectric figure of merit in ternary La3Cu3X4 (X = P, As, Sb and Bi) compounds
Authors: Pandey Tribhuwan , Parker David S.
Published: October 2017

We investigate the thermoelectric properties of the relatively unexplored rare-earth ternary compounds La3Cu3X4 (X = Bi, Sb, As, and P) using first principles electronic structure and Boltzmann transport calculations. These compounds, of which the La3Cu3Sb4 and La3Cu3Bi4 have previously been synthesized, are all predicted to be semiconductors and present a wide range of bandgaps varying from 0.24 eV (for the Bi compound) to 0.87 eV (for the P compound). We further find a mixture of light and heavy bands, which results in a high thermoelectric power factor. In addition, as discussed in our previous study (Phys. Rev. B 95 (22), 224306, 2017) at high temperatures of 1000 K these compounds exhibit lattice thermal conductivity less than 1 W/mK. The combination of low thermal conductivity and good transport properties results in a predicted ZT as high as ~1.5 for both La3Cu3P4 and La3Cu3As4, under high p-type doping. This predicted high performance makes these compounds promising candidates for high temperature thermoelectric applications and thus merits further experimental investigation.
Retinal Pigment Epithelium Sequelae Caused by Blunt Ocular Trauma: Incidence, Visual Outcome, and Associated Factors
Authors: Ahn Seong Joon , Woo Se Joon , Park Kyu Hyung , Lee Byung Ro
Published: October 2017

Vision loss can occur in eyes with blunt ocular trauma, but the causes have not been elucidated fully. We encountered cases of retinal pigment epithelium (RPE) sequelae following blunt ocular trauma associated with permanent vision loss in our cohort of patients with blunt ocular trauma. In this multicentre retrospective cohort study on 129 patients with retinal abnormalities caused by acute blunt ocular trauma, we investigated the incidence of RPE sequelae and evaluated associated factors and visual outcomes. RPE sequelae, which typically presented as hyperpigmentation within well-demarcated hypopigmented lesions, occurred in 29 (22.5%) patients within 1 month of trauma. Optical coherence tomography (OCT) revealed complete photoreceptor loss over the abnormal RPE. Final visual outcomes were significantly different between eyes with and without RPE sequelae. Logistic regression analysis revealed a significant association between the presence of subretinal fluid and RPE sequelae. In conclusion, RPE sequelae occurred in approximately 20% of patients with blunt ocular trauma and was associated with permanent photoreceptor defects and visual loss. Clinical evaluation using OCT may help predict RPE sequelae and visual outcomes in eyes with blunt trauma.
Oligomerization and ATP stimulate condensin-mediated DNA compaction
Authors: Keenholtz Ross A. , Dhanaraman Thillaivillalan , Palou Roger , Yu Jia , D’Amours Damien , Marko John F.
Published: October 2017

Large-scale chromatin remodeling during mitosis is catalyzed by a heteropentameric enzyme known as condensin. The DNA-organizing mechanism of condensin depends on the energy of ATP hydrolysis but how this activity specifically promotes proper compaction and segregation of chromosomes during mitosis remains poorly understood. Purification of budding yeast condensin reveals that it occurs not only in the classical heteropentameric “monomer” form, but that it also adopts much larger configurations consistent with oligomerization. We use a single-DNA magnetic tweezers assay to study compaction of DNA by yeast condensin, with the result that only the multimer shows ATP-enhanced DNA-compaction. The compaction reaction involves step-like events of 200 nm (600 bp) size and is strongly suppressed by forces above 1 pN, consistent with a loop-capture mechanism for initial binding and compaction. The compaction reactions are largely insensitive to DNA torsional stress. Our results suggest a physiological role for oligomerized condensin in driving gradual chromatin compaction by step-like and slow “creeping” dynamics consistent with a loop-extrusion mechanism.
Genetic diversity and structure of wild and cultivated Amorphophallus paeoniifolius populations in southwestern China as revealed by RAD-seq
Authors: Gao Yong , Yin Si , Wu Lifang , Dai Dongqin , Wang Haibo , Liu Chao , Tang Lizhou
Published: October 2017

Amorphophallus paeoniifolius, is a commercially important vegetable crop because of its high production potential. In this study, we generated a total of 166 Gb of genomic data from 16 wild and 20 cultivated A. paeoniifolius individuals in southwestern China using restriction site associated DNA sequencing (RAD-seq). We compared the genome-wide variations between the wild and cultivated populations. Wild populations exhibited higher genetic diversity than did cultivated populations based on private allele number, expected heterozygosity, observed heterozygosity and nucleotide diversity. STRUCTURE analysis, principal component analysis (PCA) and a maximum likelihood (ML) tree indicated that A. paeoniifolius populations could be divided into three groups (a cultivated group and two wild groups) with significant genetic differentiation. The low genetic diversity and shallow genetic differentiation found within cultivated populations are likely caused by continuous selection and the clonal propagation methods used during domestication. The significant differentiation between the wild populations may suggest strong genetic drift due to small populations and human disturbance. The genome-wide single nucleotide polymorphisms (SNPs) identified in our study will provide a valuable resource for further breeding improvement and effective use of the germplasm.
Eye-Head Coordination in 31 Space Shuttle Astronauts during Visual Target Acquisition
Authors: Reschke Millard F. , Kolev Ognyan I. , Clément Gilles
Published: October 2017

Between 1989 and 1995, NASA evaluated how increases in flight duration of up to 17 days affected the health and performance of Space Shuttle astronauts. Thirty-one Space Shuttle pilots participating in 17 space missions were tested at 3 different times before flight and 3 different times after flight, starting within a few hours of return to Earth. The astronauts moved their head and eyes as quickly as possible from the central fixation point to a specified target located 20°, 30°, or 60° off center. Eye movements were measured with electro-oculography (EOG). Head movements were measured with a triaxial rate sensor system mounted on a headband. The mean time to visually acquire the targets immediately after landing was 7–10% (30–34 ms) slower than mean preflight values, but results returned to baseline after 48 hours. This increase in gaze latency was due to a decrease in velocity and amplitude of both the eye saccade and head movement toward the target. Results were similar after all space missions, regardless of length.
Assessment of Variability in the SOMAscan Assay
Authors: Candia Julián , Cheung Foo , Kotliarov Yuri , Fantoni Giovanna , Sellers Brian , Griesman Trevor , Huang Jinghe , Stuccio Sarah , Zingone Adriana , Ryan Bríd M. , Tsang John S. , Biancotto Angélique
Published: October 2017

SOMAscan is an aptamer-based proteomics assay capable of measuring 1,305 human protein analytes in serum, plasma, and other biological matrices with high sensitivity and specificity. In this work, we present a comprehensive meta-analysis of performance based on multiple serum and plasma runs using the current 1.3 k assay, as well as the previous 1.1 k version. We discuss normalization procedures and examine different strategies to minimize intra- and interplate nuisance effects. We implement a meta-analysis based on calibrator samples to characterize the coefficient of variation and signal-over-background intensity of each protein analyte. By incorporating coefficient of variation estimates into a theoretical model of statistical variability, we also provide a framework to enable rigorous statistical tests of significance in intervention studies and clinical trials, as well as quality control within and across laboratories. Furthermore, we investigate the stability of healthy subject baselines and determine the set of analytes that exhibit biologically stable baselines after technical variability is factored in. This work is accompanied by an interactive web-based tool, an initiative with the potential to become the cornerstone of a regularly updated, high quality repository with data sharing, reproducibility, and reusability as ultimate goals.
Facile and sensitive detection of clenbuterol in pork using a personal glucose meter
Authors: Li Fang , Zhang Ruihua , Kang Huaibin , Hu Yonggang , Liu Yunhong , Zhu Junya
Published: October 2017

A facile and sensitive method for the detection of clenbuterol using a personal glucose meter was reported.
Simultaneous determination of bisphenol A and tetrabromobisphenol A in tea using a modified QuEChERS sample preparation method coupled with liquid chromatography-tandem mass spectrometry
Authors: Gao Guanwei , Chen Hongping , Zhu Li , Chai Yunfeng , Ma Guicen , Wang Chen , Hao Zhenxia , Liu Xin , Lu Chengyin
Published: October 2017

A rapid and sensitive method for the simultaneous determination of bisphenol A (BPA) and tetrabromobisphenol A (TBBPA) in tea using liquid chromatography-tandem mass spectrometry (LC-MS/MS) was developed and validated.
Controlled fabrication of osmium nanocrystals by electron, laser and microwave irradiation and characterisation by microfocus X-ray absorption spectroscopy
Authors: Pitto-Barry Anaïs , Geraki Kalotina , Horbury Michael D. , Stavros Vasilios G. , Mosselmans J. Frederick W. , Walton Richard I. , Sadler Peter J. , Barry Nicolas P. E.
Published: October 2017

Osmium nanocrystals are fabricatedvia3 methods and characterised by XAS, revealing different surface oxidation and metallicities depending on their fabrication technique.
Coherent diffractive imaging of graphite nanoparticles using a tabletop EUV source
Authors: Xuan Truong Nguyen , Strashnov Ilya , Whittaker Eric , Zhong Xiang Li , Denecke Melissa A.
Published: October 2017

Coherent diffractive imaging of nanographites using a tabletop EUV source reveals the structural information and possible absorption effects.
The internal structure of PMETAC brush/gold nanoparticle composites: a neutron and X-ray reflectivity study
Authors: Kesal D. , Christau S. , Trapp M. , Krause P. , von Klitzing R.
Published: October 2017

The amount and distribution of gold nanoparticles within a polymer brush matrix can be changed by altering the electrostatic interaction between particle–particle as well as particle–brush.
Extension of catalyst lifetime by doping of Ce in Ni-loaded acid-washed Shengli lignite char for biomass catalytic gasification
Authors: Ren Jie , Cao Jing-Pei , Zhao Xiao-Yan , Wei Fu , Zhu Chen , Wei Xian-Yong
Published: October 2017

Preparation and lifetime extension of modified lignite char loaded with Ni by doping of Ce using a co-impregnation method for biomass gasification.
Systematic metabolic engineering of Corynebacterium glutamicum for the industrial-level production of optically pure d-(−)-acetoin
Authors: Mao Yufeng , Fu Jing , Tao Ran , Huang Can , Wang Zhiwen , Tang Ya-Jie , Chen Tao , Zhao Xueming
Published: October 2017

Acetoin is a high-value-added industrial product and a promising bio-based platform chemical.
Reversible switching of solid-state luminescence by heat-induced interconversion of molecular packing
Authors: Naeem Karattu Chali , Nair Vijayakumar C.
Published: October 2017

Reversible solid-state luminescence switching in divinylbenzene derivatives by heat-induced interconversion of molecular packing is studied. The effect of mechanical stimuli on the molecular assemblies is also described.
High throughput fabrication of cell spheroids by templating water-in-water Pickering emulsions
Authors: Das Anupam A. K. , Filby Benjamin W. , Geddes Daniel A. , Legrande Deborah , Paunov Vesselin N.
Published: October 2017

We report a simple technique for the high throughput generation of tissue spheroids based on the encapsulation of dispersed adherent cells in particle-stabilized water-in-water emulsions.
Fluorine-free preparation of titanium carbide MXene quantum dots with high near-infrared photothermal performances for cancer therapy
Authors: Yu Xinghua , Cai Xingke , Cui Haodong , Lee Seung-Wuk , Yu Xue-Feng , Liu Bilu
Published: October 2017

Titanium carbide MXene QDs were synthesized using a newly-developed fluorine-free method. Significantly, they exhibit very high extinction coefficient and photothermal conversion efficiency, and great biocompatibility, showing high potential for PTT applications.
2D and 3D surface photopatterning via laser-promoted homopolymerization of a perfluorophenyl azide-substituted BODIPY
Authors: Raffy Guillaume , Bofinger Robin , Tron Arnaud , Guerzo André Del , McClenaghan Nathan D. , Vincent Jean-Marc
Published: October 2017

A direct laser-writing methodology, harnessing the homopolymerization of a perfluorophenyl-azide BODIPY molecule, which forms red fluorescent nanostructures of controlled height is described.
A new approach to thiazoloisoindigo and derivatives using a lithium tetramethylpiperidine promoted cyclization to thiazoloisatin
Authors: Li Chenchen , Zhang Huanrui , Mirie Samuel , Peng Jiawei , Cai Mian , Wang Xiao , Lan Zhenggang , Wan Xiaobo
Published: October 2017

Thiazoloisoindigo and its derivatives were synthesized for the first time from thiazoloisatin, which was obtained via a novel cyclization strategy.