bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acidity-Controlled Conducting Polymer Films for Organic Thermoelectric Devices with Horizontal and Vertical Architectures
Authors: Lee Woongki , Song Myeonghun , Park Soohyung , Nam Sungho , Seo Jooyeok , Kim Hwajeong , Kim Youngkyoo 
Published: September 2016

AbstractOrganic thermoelectric devices (OTEDs) are recognized one of the next generation energy conversion platforms because of their huge potentials for securing electricity continuously from even tiny heat sources in our daily life. The advantage of OTEDs can be attributable to the design freedom in device shapes and the low-cost fabrication by employing solution coating processes at low temperatures. As one of the major OTE materials to date, poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) has been used, but no study has been yet carried out on its acidity control even though the acidic components in OTEDs can seriously affect the device performance upon operation. Here we demonstrate that the addition of aniline (a weak base) can control the acidity of PEDOT:PSS and enhance the performance of OTEDs. In particular, the vertical OTEDs with aniline-doped PEDOT:PSS films (active area = 1.0 cm2) could continuously generate electricity (0.06 nW) even at low temperatures (<38 °C) when they were mounted on a desk lamp (power = 24 W).
A general and efficient strategy for generating the stable enzymes
Authors: Zhang Xiao-Fei , Yang Guang-Yu , Zhang Yong , Xie Yuan , Withers Stephen G. , Feng Yan 
Published: September 2016

AbstractThe local flexibility of an enzyme’s active center plays pivotal roles in catalysis, however, little is known about how the flexibility of these flexible residues affects stability. In this study, we proposed an active center stabilization (ACS) strategy to improve the kinetic thermostability of Candida rugosa lipase1. Based on the B-factor ranking at the region ~10 Å within the catalytic Ser209, 18 residues were selected for site-saturation mutagenesis. Based on three-tier high-throughput screening and ordered recombination mutagenesis, the mutant VarB3 (F344I/F434Y/F133Y/F121Y) was shown to be the most stable, with a 40-fold longer in half-life at 60 °C and a 12.7 °C higher Tm value than that of the wild type, without a decrease in catalytic activity. Further analysis of enzymes with different structural complexities revealed that focusing mutations on the flexible residues within around 10 Å of the catalytic residue might increase the success rate for enzyme stabilization. In summary, this study identifies a panel of flexible residues within the active center that affect enzyme stability. This finding not only provides clues regarding the molecular evolution of enzyme stability but also indicates that ACS is a general and efficient strategy for exploring the functional robustness of enzymes for industrial applications.
Compartmentalized gene expression profiling of receptive endometrium reveals progesterone regulated ENPP3 is differentially expressed and secreted in glycosylated form
Authors: Boggavarapu Nageswara Rao , Lalitkumar Sujata , Joshua Vijay , Kasvandik Sergo , Salumets Andres , Lalitkumar Parameswaran Grace , Gemzell-Danielsson Kristina 
Published: September 2016

AbstractThe complexity of endometrial receptivity at the molecular level needs to be explored in detail to improve the management of infertility. Here, differential expression of transcriptomes in receptive endometrial glands and stroma revealed Ectonucleotide Pyrophosphatase/Phosphodiesterase 3 (ENPP3) as a progesterone regulated factor and confirmed by various methods, both at mRNA and protein level. The involvement of ENPP3 in embryo attachment was tested in an in vitro model for human embryo implantation. Interestingly, there was high expression of ENPP3 mRNA in stroma but not protein. Presence of N-glycosylated ENPP3 in receptive phase uterine fluid in women confirms its regulation by progesterone and makes it possible to use in a non-invasive test of endometrial receptivity.
Two-step phase-shifting SPIDER
Authors: Zheng Shuiqin , Cai Yi , Pan Xinjian , Zeng Xuanke , Li Jingzhen , Li Ying , Zhu Tianlong , Lin Qinggang , Xu Shixiang 
Published: September 2016

AbstractComprehensive characterization of ultrafast optical field is critical for ultrashort pulse generation and its application. This paper combines two-step phase-shifting (TSPS) into the spectral phase interferometry for direct electric-field reconstruction (SPIDER) to improve the reconstruction of ultrafast optical-fields. This novel SPIDER can remove experimentally the dc portion occurring in traditional SPIDER method by recording two spectral interferograms with π phase-shifting. As a result, the reconstructed results are much less disturbed by the time delay between the test pulse replicas and the temporal widths of the filter window, thus more reliable. What is more, this SPIDER can work efficiently even the time delay is so small or the measured bandwidth is so narrow that strong overlap happens between the dc and ac portions, which allows it to be able to characterize the test pulses with complicated temporal/spectral structures or narrow bandwidths.
Effective vitrification and warming of porcine embryos using a pH-stable, chemically defined medium
Authors: Cuello Cristina , Martinez Cristina A. , Nohalez Alicia , Parrilla Inmaculada , Roca Jordi , Gil Maria A. , Martinez Emilio A. 
Published: September 2016

AbstractThe use of pH-stable media would simplify embryo vitrification and the warming of porcine embryos and might facilitate the application of embryo transfer in practice. In this work, we investigated whether a pH-stable basal medium constituted of Tyrode’s lactate medium, polyvinyl alcohol, and HEPES for buffering was suitable for porcine embryo vitrification warming in place of the conventional gas-equilibrated media. A high percentage (>90%) of embryos survived vitrification and warming in this medium, achieving in vitro survival rates similar to embryos vitrified-warmed using the conventional protocol and their fresh counterparts. The pH-stable medium did not affect the in vivo developmental competence of the vitrified-warmed embryos. A farrowing rate of 71.4% (5/7) with 10.4 ± 3.1 piglets born was obtained for the embryos vitrified and warmed in this medium and transferred to selected recipients. This medium will enable the use of simple, safe and standardized protocols for the vitrification and warming of porcine embryos for optimal embryo survival and quality when applied under field conditions. This study opens new possibilities for the widespread use of embryo transfer in pigs.
Gondwanan conifer clones imperilled by bushfire
Authors: Worth James R. P. , Sakaguchi Shota , Rann Karl D. , Bowman Clarence J. W. , Ito Motomi , Jordan Gregory J. , Bowman David M. J. S. 
Published: September 2016

AbstractGlobal increases in fire frequency driven by anthropogenic greenhouse emissions and land use change could threaten unique and ancient species by creeping into long-term fire refugia. The perhumid and mountainous western half of Tasmania is a globally important refugium for palaeo-endemic, fire intolerant lineages, especially conifers. Reproductive strategy will be crucial to the resilience of these organisms under warmer, dryer and more fire prone climates. This study analysed clonal versus sexual reproduction in old growth plots dominated by the palaeo-endemic conifer Athrotaxis cupressoides (Cupressaceae), a species that lacks any traits to tolerate frequent landscape fire. Across most of the seven plots the amount of sexually derived individuals was lower than clonally derived with, on average, 60% of all stems belonging to the same multi-locus lineage (MLL) (i.e. were clonal). Some MLLs were large spanning over 10 s of metres and consisted of up to 62 stems. The high mortality after fire and the rarity of sexual regeneration means that the range of this fire-intolerant species is likely to contract under enhanced fire regimes and has a limited capacity to disperse via seed to available fire refugia in the landscape.
Differential expression of miR-184 in temporal lobe epilepsy patients with and without hippocampal sclerosis – Influence on microglial function
Authors: Danis Bénédicte , van Rikxoort Marijke , Kretschmann Anita , Zhang Jiong , Godard Patrice , Andonovic Lidija , Siegel Franziska , Niehusmann Pitt , Hanon Etienne , Delev Daniel , von Lehe Marec , Kaminski Rafal M. , Pfeifer Alexander , Foerch Patrik 
Published: September 2016

AbstractEpilepsy is one of the most common neurological disorders characterized by recurrent seizures due to neuronal hyperexcitability. Here we compared miRNA expression patterns in mesial temporal lobe epilepsy with and without hippocampal sclerosis (mTLE + HS and mTLE −HS) to investigate the regulatory mechanisms differentiating both patient groups. Whole genome miRNA sequencing in surgically resected hippocampi did not reveal obvious differences in expression profiles between the two groups of patients. However, one microRNA (miR-184) was significantly dysregulated, which was confirmed by qPCR. We observed that overexpression of miR-184 inhibited cytokine release after LPS stimulation in primary microglial cells, while it did not affect the viability of murine primary neurons and primary astrocytes. Pathway analysis revealed that miR-184 is potentially involved in the regulation of inflammatory signal transduction and apoptosis. Dysregulation of some the potential miR-184 target genes was confirmed by qPCR and 3′UTR luciferase reporter assay. The reduced expression of miR-184 observed in patients with mTLE + HS together with its anti-inflammatory effects indicate that miR-184 might be involved in the modulation of inflammatory processes associated with hippocampal sclerosis which warrants further studies elucidating the role of miR-184 in the pathophysiology of mTLE.
Ultra-stable clock laser system development towards space applications
Authors: Świerad Dariusz , Häfner Sebastian , Vogt Stefan , Venon Bertrand , Holleville David , Bize Sébastien , Kulosa André , Bode Sebastian , Singh Yeshpal , Bongs Kai , Rasel Ernst Maria , Lodewyck Jérôme , Le Targat Rodolphe , Lisdat Christian , Sterr Uwe 
Published: September 2016

AbstractThe increasing performance of optical lattice clocks has made them attractive for scientific applications in space and thus has pushed the development of their components including the interrogation lasers of the clock transitions towards being suitable for space, which amongst others requires making them more power efficient, radiation hardened, smaller, lighter as well as more mechanically stable. Here we present the development towards a space-compatible interrogation laser system for a strontium lattice clock constructed within the Space Optical Clock (SOC2) project where we have concentrated on mechanical rigidity and size. The laser reaches a fractional frequency instability of 7.9 × 10−16 at 300 ms averaging time. The laser system uses a single extended cavity diode laser that gives enough power for interrogating the atoms, frequency comparison by a frequency comb and diagnostics. It includes fibre link stabilisation to the atomic package and to the comb. The optics module containing the laser has dimensions 60 × 45 × 8 cm3; and the ultra-stable reference cavity used for frequency stabilisation with its vacuum system takes 30 × 30 × 30 cm3. The acceleration sensitivities in three orthogonal directions of the cavity are 3.6 × 10−10/g, 5.8 × 10−10/g and 3.1 × 10−10/g, where g ≈ 9.8 m/s2 is the standard gravitational acceleration.
Protein characterization of intracellular target-sorted, formalin-fixed cell subpopulations
Authors: Sadick Jessica S. , Boutin Molly E. , Hoffman-Kim Diane , Darling Eric M. 
Published: September 2016

AbstractCellular heterogeneity is inherent in most human tissues, making the investigation of specific cell types challenging. Here, we describe a novel, fixation/intracellular target-based sorting and protein extraction method to provide accurate protein characterization for cell subpopulations. Validation and feasibility tests were conducted using homogeneous, neural cell lines and heterogeneous, rat brain cells, respectively. Intracellular proteins of interest were labeled with fluorescent antibodies for fluorescence-activated cell sorting. Reproducible protein extraction from fresh and fixed samples required lysis buffer with high concentrations of Tris-HCl and sodium dodecyl sulfate as well as exposure to high heat. No deterioration in protein amount or quality was observed for fixed, sorted samples. For the feasibility experiment, a primary rat subpopulation of neuronal cells was selected for based on high, intracellular β-III tubulin signal. These cells showed distinct protein expression differences from the unsorted population for specific (phosphorylated tau) and non-specific (total tau) protein targets. Our approach allows for determining more accurate protein profiles directly from cell types of interest and provides a platform technology in which any cell subpopulation can be biochemically investigated.
MALDI-TOF-MS reveals differential N-linked plasma- and IgG-glycosylation profiles between mothers and their newborns
Authors: Jansen Bas C. , Bondt Albert , Reiding Karli R. , Scherjon Sicco A. , Vidarsson Gestur , Wuhrer Manfred 
Published: September 2016

AbstractDuring pregnancy, the mother provides multiple nutrients and substances to the foetus, with maternal immunoglobulin G (IgG) being actively transported to the foetus. Newborns depend on maternal IgG for immune-protection in their first months. The glycosylation of IgG has been shown to influence its dynamics, e.g. receptor binding. While minor differences in IgG glycosylation have been found between IgG derived from maternal blood and umbilical cord blood (UC) of newborn children, the differential glycosylation of maternal and UC plasma has hitherto not been studied. Here, we studied the N-glycosylation of IgG and total plasma proteome of both maternal and UC plasma of 42 pairs of mothers and newborn children. A total of 37 N-glycans were quantified for IgG and 45 for the total plasma N-glycome (TPNG). The study showed slightly higher levels of galactosylation for UC IgG than maternal IgG, confirming previous results, as well as lower bisection and sialylation. Furthermore, the TPNG results showed lower values for galactosylation and sialylation and higher values for fucosylation in the UC plasma. In conclusion, this study presents some novel insights into IgG glycosylation differences as well as the first broad overview of the differential plasma glycosylation between mothers and newborns.
Highly conductive and pure gold nanostructures grown by electron beam induced deposition
Authors: Shawrav Mostafa M. , Taus Philipp , Wanzenboeck Heinz D. , Schinnerl M. , Stöger-Pollach M. , Schwarz S. , Steiger-Thirsfeld A. , Bertagnolli Emmerich 
Published: September 2016

AbstractThis work introduces an additive direct-write nanofabrication technique for producing extremely conductive gold nanostructures from a commercial metalorganic precursor. Gold content of 91 atomic % (at. %) was achieved by using water as an oxidative enhancer during direct-write deposition. A model was developed based on the deposition rate and the chemical composition and it explains the surface processes that lead to the increases in gold purity and deposition yield. Co-injection of an oxidative enhancer enabled Focused Electron Beam Induced Deposition (FEBID)—a maskless, resistless deposition method for three dimensional (3D) nanostructures—to directly yield pure gold in a single process step, without post-deposition purification. Gold nanowires displayed resistivity down to 8.8 μΩ cm. This is the highest conductivity achieved so far from FEBID and it opens the possibility of applications in nanoelectronics, such as direct-write contacts to nanomaterials. The increased gold deposition yield and the ultralow carbon level will facilitate future applications such as the fabrication of 3D nanostructures in nanoplasmonics and biomolecule immobilization.
Emergence of global scaling behaviour in the coupled Earth-atmosphere interaction
Authors: Fallah Bijan , Saberi Abbas Ali , Sodoudi Sahar 
Published: September 2016

AbstractScale invariance property in the global geometry of Earth may lead to a coupled interactive behaviour between various components of the climate system. One of the most interesting correlations exists between spatial statistics of the global topography and the temperature on Earth. Here we show that the power-law behaviour observed in the Earth topography via different approaches, resembles a scaling law in the global spatial distribution of independent atmospheric parameters. We report on observation of scaling behaviour of such variables characterized by distinct universal exponents. More specifically, we find that the spatial power-law behaviour in the fluctuations of the near surface temperature over the lands on Earth, shares the same universal exponent as of the global Earth topography, indicative of the global persistent role of the static geometry of Earth to control the steady state of a dynamical atmospheric field. Such a universal feature can pave the way to the theoretical understanding of the chaotic nature of the atmosphere coupled to the Earth’s global topography.
Histone Deacetylase Inhibitor Phenylbutyrate Exaggerates Heart Failure in Pressure Overloaded Mice independently of HDAC inhibition
Authors: Ma Jing , Luo Tao , Zeng Zhi , Fu Haiying , Asano Yoshihiro , Liao Yulin , Minamino Tetsuo , Kitakaze Masafumi 
Published: September 2016

Abstract4-Sodium phenylbutyrate (PBA) has been reported to inhibit endoplasmic reticulum stress and histone deacetylation (HDAC), both of which are novel therapeutic targets for cardiac hypertrophy and heart failure. However, it is unclear whether PBA can improve heart function. Here, we tested the effects of PBA and some other HDAC inhibitors on cardiac dysfunction induced by pressure overload. Transverse aortic constriction (TAC) was performed on male C57BL/6 mice. PBA treatment (100 mg/kg, 6 weeks) unexpectedly led to a higher mortality, exacerbated cardiac remodelling and dysfunction. Similar results were noted in TAC mice treated with butyrate sodium (BS), a PBA analogue. In contrast, other HDAC inhibitors, valproic acid (VAL) and trichostatin A (TSA), improved the survival. All four HDAC inhibitors induced histone H3 acetylation and inhibited HDAC total activity. An individual HDAC activity assay showed that rather than class IIa members (HDAC4 and 7), PBA and BS predominantly inhibited class I members (HDAC2 and 8), whereas VAL and TSA inhibited all of them. These findings indicate that PBA and BS accelerate cardiac hypertrophy and dysfunction, whereas VAL and TSA have opposing effects.
Paraspeckles modulate the intranuclear distribution of paraspeckle-associated Ctn RNA
Authors: Anantharaman Aparna , Jadaliha Mahdieh , Tripathi Vidisha , Nakagawa Shinichi , Hirose Tetsuro , Jantsch Michael F. , Prasanth Supriya G. , Prasanth Kannanganattu V. 
Published: September 2016

AbstractParaspeckles are sub-nuclear domains that are nucleated by long noncoding RNA Neat1. While interaction of protein components of paraspeckles and Neat1 is understood, there is limited information on the interaction of non-structural RNA components with paraspeckles. Here, by varying paraspeckle number and size, we investigate how paraspeckles influence the nuclear organization of their non-structural RNA component Ctn RNA. Our results show that Ctn RNA remains nuclear-retained in the absence of intact paraspeckles, suggesting that they do not regulate nuclear retention of Ctn RNA. In the absence of Neat1, Ctn RNA continues to interact with paraspeckle protein NonO to form residual nuclear foci. In addition, in the absence of Neat1-nucleated paraspeckles, a subset of Ctn RNA localizes to the perinucleolar regions. Concomitant with increase in number of paraspeckles, transcriptional reactivation resulted in increased number of paraspeckle-localized Ctn RNA foci. Similar to Neat1, proteasome inhibition altered the localization of Ctn RNA, where it formed enlarged paraspeckle-like foci. Super-resolution structured illumination microscopic analyses revealed that in paraspeckles, Ctn RNA partially co-localized with Neat1, and displayed a more heterogeneous intra-paraspeckle localization. Collectively, these results show that while paraspeckles do not influence nuclear retention of Ctn RNA, they modulate its intranuclear compartmentalization.
CRHunter: integrating multifaceted information to predict catalytic residues in enzymes
Authors: Sun Jun , Wang Jia , Xiong Dan , Hu Jian , Liu Rong 
Published: September 2016

AbstractA variety of algorithms have been developed for catalytic residue prediction based on either feature- or template-based methodology. However, no studies have systematically compared these two strategies and further considered whether their combination could improve the prediction performance. Herein, we developed an integrative algorithm named CRHunter by simultaneously using the complementarity between feature- and template-based methodologies and that between structural and sequence information. Several novel structural features were generated by the Delaunay triangulation and Laplacian transformation of enzyme structures. Combining these features with traditional descriptors, we invented two support vector machine feature predictors based on both structural and sequence information. Furthermore, we established two template predictors using structure and profile alignments. Evaluated on datasets with different levels of homology, our feature predictors achieve relatively stable performance, whereas our template predictors yield poor results when the homological relationships become weak. Nevertheless, the hybrid algorithm CRHunter consistently achieves optimal performance among all our predictors. We also illustrate that our methodology can be applied to the predicted structures of enzymes. Compared with state-of-the-art methods, CRHunter yields comparable or better performance on various datasets. Finally, the application of this algorithm to structural genomics targets sheds light on solved protein structures with unknown functions.
Expression profiling of cutaneous squamous cell carcinoma with perineural invasion implicates the p53 pathway in the process
Authors: Warren Timothy A. , Broit Natasa , Simmons Jacinta L. , Pierce Carly J. , Chawla Sharad , Lambie Duncan L. J. , Quagliotto Gary , Brown Ian S. , Parsons Peter G. , Panizza Benedict J. , Boyle Glen M. 
Published: September 2016

AbstractSquamous cell carcinoma (SCC) is the second most common cancer worldwide and accounts for approximately 30% of all keratinocyte cancers. The vast majority of cutaneous SCCs of the head and neck (cSCCHN) are readily curable with surgery and/or radiotherapy unless high-risk features are present. Perineural invasion (PNI) is recognized as one of these high-risk features. The molecular changes during clinical PNI in cSCCHN have not been previously investigated. In this study, we assessed the global gene expression differences between cSCCHN with or without incidental or clinical PNI. The results of the analysis showed signatures of gene expression representative of activation of p53 in tumors with PNI compared to tumors without, amongst other alterations. Immunohistochemical staining of p53 showed cSCCHN with clinical PNI to be more likely to exhibit a diffuse over-expression pattern, with no tumors showing normal p53 staining. DNA sequencing of cSCCHN samples with clinical PNI showed no difference in mutation number or position with samples without PNI, however a significant difference was observed in regulators of p53 degradation, stability and activity. Our results therefore suggest that cSCCHN with clinical PNI may be more likely to contain alterations in the p53 pathway, compared to cSCCHN without PNI.