bluuebunny/crossref_metadata_2025_split huggingface dataset:
Visualization of synaptic domains in the Drosophila brain by magnetic resonance microscopy at 10 micron isotropic resolution
Authors: Lee Choong H. , Blackband Stephen J. , Fernandez-Funez Pedro 
Published: March 2015

AbstractUnderstanding the complex architecture, connectivity and pathology of the human brain is a major application of magnetic resonance imaging (MRI). However, the cellular basis of MR signal is still poorly understood. The advent of MR microscopy (MRM) enables imaging biological samples at cellular resolution, helping to interpret the nature of MR signal at the cellular level. In this regard, the small Drosophila brain can reveal key aspects of MR signal through the visualization of complex, intact neuronal structures in their native spatial arrangement. Applying state-of-the-art MR technology, we imaged fixed Drosophila heads at 10 μm isotropic resolution by two endogenously contrasted MRM sequences. The improved MRM sensitivity described here delivered the highest 3D resolution of an intact animal head reported so far. 3D fast low angle shot (FLASH) revealed strong signal in most internal tissues, particularly in the brain cortex, which contains the cell bodies of neurons and glia. Remarkably, 3D diffusion weighted imaging (DWI) delivered unprecedented contrast within the modular brain neuropil, revealing hyperintense signal in synapse-rich microdomains. Thus, the complex Drosophila brain revealed unknown features of FLASH and DWI with potential applications in characterizing the structure and pathology of the mammalian brain.
Novel genetic variants in differentiated thyroid cancer and assessment of the cumulative risk
Authors: Figlioli Gisella , Chen Bowang , Elisei Rossella , Romei Cristina , Campo Chiara , Cipollini Monica , Cristaudo Alfonso , Bambi Franco , Paolicchi Elisa , Hoffmann Per , Herms Stefan , Kalemba Michał , Kula Dorota , Pastor Susana , Marcos Ricard , Velázquez Antonia , Jarząb Barbara , Landi Stefano , Hemminki Kari , Gemignani Federica , Försti Asta 
Published: March 2015

AbstractA genome-wide association study (GWAS) performed on a high-incidence Italian population followed by replications on low-incidence cohorts suggested a strong association of differentiated thyroid cancer (DTC) with single nucleotide polymorphisms (SNPs) at 9q22.33, 2q35, 20q11.22-q12 and 14q24.3. Moreover, six additional susceptibility loci were associated with the disease only among Italians. The present study had two aims, first to identify loci involved in DTC risk and then to assess the cumulative effect of the SNPs identified so far in the Italian population. The combined analysis of the previous GWAS and the present Italian study provided evidence of association with rs7935113 (GALNTL4, OR = 1.36, 95%CI 1.20–1.53, p-value = 7.41 × 10−7) and rs1203952 (FOXA2, OR = 1.29, 95%CI 1.16–1.44, p-value = 4.42 × 10−6). Experimental ENCODE and eQTL data suggested that both SNPs may influence the closest genes expression through a differential recruitment of transcription factors. The assessment of the cumulative risk of eleven SNPs showed that DTC risk increases with an increasing number of risk alleles (p-trend = 3.13 × 10−47). Nonetheless, only a small fraction (about 4% on the disease liability scale) of DTC is explained by these SNPs. These data are consistent with a polygenic model of DTC predisposition and highlight the importance of association studies in the discovery of the disease hereditability.
Metabolomics integrated elementary flux mode analysis in large metabolic networks
Authors: Gerstl Matthias P. , Ruckerbauer David E. , Mattanovich Diethard , Jungreuthmayer Christian , Zanghellini Jürgen 
Published: March 2015

AbstractElementary flux modes (EFMs) are non-decomposable steady-state pathways in metabolic networks. They characterize phenotypes, quantify robustness or identify engineering targets. An EFM analysis (EFMA) is currently restricted to medium-scale models, as the number of EFMs explodes with the network's size. However, many topologically feasible EFMs are biologically irrelevant. We present thermodynamic EFMA (tEFMA), which calculates only the small(er) subset of thermodynamically feasible EFMs. We integrate network embedded thermodynamics into EFMA and show that we can use the metabolome to identify and remove thermodynamically infeasible EFMs during an EFMA without losing biologically relevant EFMs. Calculating only the thermodynamically feasible EFMs strongly reduces memory consumption and program runtime, allowing the analysis of larger networks. We apply tEFMA to study the central carbon metabolism of E. coli and find that up to 80% of its EFMs are thermodynamically infeasible. Moreover, we identify glutamate dehydrogenase as a bottleneck, when E. coli is grown on glucose and explain its inactivity as a consequence of network embedded thermodynamics. We implemented tEFMA as a Java package which is available for download at https://github.com/mpgerstl/tEFMA.
Lack of stress responses to long-term effects of corticosterone in Caps2 knockout mice
Authors: Mishima Yuriko , Shinoda Yo , Sadakata Tetsushi , Kojima Masami , Wakana Shigeharu , Furuichi Teiichi 
Published: March 2015

AbstractChronic stress is associated with anxiety and depressive disorders and can cause weight gain. Ca2+-dependent activator protein for secretion 2 (CAPS2) is involved in insulin release. Caps2 knockout (KO) mice exhibit decreased body weight, reduced glucose-induced insulin release and abnormal psychiatric behaviors. We chronically administered the stress hormone corticosterone (CORT), which induces anxiety/depressive-like behavior and normally increases plasma insulin levels, via the drinking water for 10 weeks and we examined the stress response in KO mice. Chronic CORT exposure inhibited stress-induced serum CORT elevation in wild-type (WT) mice, but not in KO mice. Poor weight gain in CORT-treated animals was observed until week 6 in WT mice, but persisted for the entire duration of the experiment in KO mice, although there is no difference in drug*genotype interaction. Among KO mice, food consumption was unchanged, while water consumption was higher, over the duration of the experiment in CORT-treated animals, compared with untreated animals. Moreover, serum insulin and leptin levels were increased in CORT-treated WT mice, but not in KO mice. Lastly, both WT and KO mice displayed anxiety/depressive-like behavior after CORT administration. These results suggest that Caps2 KO mice have altered endocrine responses to CORT administration, while maintaining CORT-induced anxiety/depressive-like behavior.
Encapsulation of S/SWNT with PANI Web for Enhanced Rate and Cycle Performance in Lithium Sulfur Batteries
Authors: Kim Joo Hyun , Fu Kun , Choi Junghyun , Kil Kichun , Kim Jeonghyun , Han Xiaogang , Hu Liangbing , Paik Ungyu 
Published: March 2015

AbstractLithium-sulfur batteries show great potential to compete with lithium-ion batteries due to the fact that sulfur can deliver a high theoretical capacity of 1672 mAh/g and a high theoretical energy density of 2500 Wh/kg. But it has several problems to be solved in order to achieve high sulfur utilization with high Coulombic efficiency and long cycle life of Li-S batteries. These problems are mainly caused by the dissoluble polysulfide species, which are a series of complex reduced sulfur products, associating with shuttle effect between electrodes as well as side reactions on lithium metal anode. To alleviate these challenges, we developed a sulfur-carbon nanotube (S/SWNT) composite coated with polyaniline (PANI) polymer as polysulfide block to achieve high sulfur utilization, high Coulombic efficiency and long cycle life. The PANI coated S/SWNT composite showed a superior specific capacity of 1011 mAh/g over 100 cycles and a good rate retention, demonstrating the synergic contribution of porous carbon and conducting polymer protection to address challenges underlying sulfur cathode.
Competition between surface modification and abrasive polishing: a method of controlling the surface atomic structure of 4H-SiC (0001)
Authors: Deng Hui , Endo Katsuyoshi , Yamamura Kazuya 
Published: March 2015

AbstractThe surface atomic step-terrace structure of 4H-SiC greatly affects its performance in power device applications. On the basis of the crystal structure of 4H-SiC, we propose the generation mechanism of the a-b-a*-b* type, a-b type and a-a type step-terrace structures. We demonstrate that the step-terrace structure of SiC can be controlled by adjusting the balance between chemical modification and physical removal in CeO2 slurry polishing. When chemical modification plays the main role in the polishing of SiC, the a-b-a*-b* type step-terrace structure can be generated. When the roles of physical removal and chemical modification have similar importance, the a-b-a*-b* type step-terrace structure changes to the a-b type. When physical removal is dominant, the uniform a-a type step-terrace structure can be generated.
Characterization and expression of the cytochrome P450 gene family in diamondback moth, Plutella xylostella (L.)
Authors: Yu Liying , Tang Weiqi , He Weiyi , Ma Xiaoli , Vasseur Liette , Baxter Simon W. , Yang Guang , Huang Shiguo , Song Fengqin , You Minsheng 
Published: March 2015

AbstractCytochrome P450 monooxygenases are present in almost all organisms and can play vital roles in hormone regulation, metabolism of xenobiotics and in biosynthesis or inactivation of endogenous compounds. In the present study, a genome-wide approach was used to identify and analyze the P450 gene family of diamondback moth, Plutella xylostella, a destructive worldwide pest of cruciferous crops. We identified 85 putative cytochrome P450 genes from the P. xylostella genome, including 84 functional genes and 1 pseudogene. These genes were classified into 26 families and 52 subfamilies. A phylogenetic tree constructed with three additional insect species shows extensive gene expansions of P. xylostella P450 genes from clans 3 and 4. Gene expression of cytochrome P450s was quantified across multiple developmental stages (egg, larva, pupa and adult) and tissues (head and midgut) using P. xylostella strains susceptible or resistant to insecticides chlorpyrifos and fiprinol. Expression of the lepidopteran specific CYP367s predominantly occurred in head tissue suggesting a role in either olfaction or detoxification. CYP340s with abundant transposable elements and relatively high expression in the midgut probably contribute to the detoxification of insecticides or plant toxins in P. xylostella. This study will facilitate future functional studies of the P. xylostella P450s in detoxification.
Electrodeposition of ZnO window layer for an all-atmospheric fabrication process of chalcogenide solar cell
Authors: Tsin Fabien , Venerosy Amélie , Vidal Julien , Collin Stéphane , Clatot Johnny , Lombez Laurent , Paire Myriam , Borensztajn Stephan , Broussillou Cédric , Grand Pierre Philippe , Jaime Salvador , Lincot Daniel , Rousset Jean 
Published: March 2015

AbstractThis paper presents the low cost electrodeposition of a transparent and conductive chlorine doped ZnO layer with performances comparable to that produced by standard vacuum processes. First, an in-depth study of the defect physics by ab-initio calculation shows that chlorine is one of the best candidates to dope the ZnO. This result is experimentally confirmed by a complete optical analysis of the ZnO layer deposited in a chloride rich solution. We demonstrate that high doping levels (>1020 cm−3) and mobilities (up to 20 cm2 V−1 s−1) can be reached by insertion of chlorine in the lattice. The process developed in this study has been applied on a CdS/Cu(In,Ga)(Se,S)2 p-n junction produced in a pilot line by a non vacuum process, to be tested as solar cell front contact deposition method. As a result efficiency of 14.3% has been reached opening the way of atmospheric production of Cu(In,Ga)(Se,S)2 solar cell.
Inverted Quantum Dot Light Emitting Diodes using Polyethylenimine ethoxylated modified ZnO
Authors: Kim Hong Hee , Park Soohyung , Yi Yeonjin , Son Dong Ick , Park Cheolmin , Hwang Do Kyung , Choi Won Kook 
Published: March 2015

AbstractColloidal quantum dots (QDs) are an emerging class of new materials due to their unique physical properties. In particular, colloidal QD based light emitting diodes (QDLEDs) have been extensively studied and developed for the next generation displays and solid-state lighting. Among a number of approaches to improve performance of the QDLEDs, the most practical one is optimization of charge transport and charge balance in the recombination region. Here, we suggest a polyethylenimine ethoxylated (PEIE) modified ZnO nanoparticles (NPs) as electron injection and transport layer for inverted structure red CdSe-ZnS based QDLED. The PEIE surface modifier, incorporated on the top of the ZnO NPs film, facilitates the enhancement of both electron injection into the CdSe-ZnS QD emissive layer by lowering the workfunction of ZnO from 3.58 eV to 2.87 eV and charge balance on the QD emitter. As a result, this device exhibits a low turn-on voltage of 2.0–2.5 V and has maximum luminance and current efficiency values of 8600 cd/m2 and current efficiency of 1.53 cd/A, respectively. The same scheme with ZnO NPs/PEIE layer has also been used to successfully fabricate green, blue and white QDLEDs.
Epigenetic Biomarker to Support Classification into Pluripotent and Non-Pluripotent Cells
Authors: Lenz Michael , Goetzke Roman , Schenk Arne , Schubert Claudia , Veeck Jürgen , Hemeda Hatim , Koschmieder Steffen , Zenke Martin , Schuppert Andreas , Wagner Wolfgang 
Published: March 2015

AbstractQuality control of human induced pluripotent stem cells (iPSCs) can be performed by several methods. These methods are usually relatively labor-intensive, difficult to standardize, or they do not facilitate reliable quantification. Here, we describe a biomarker to distinguish between pluripotent and non-pluripotent cells based on DNA methylation (DNAm) levels at only three specific CpG sites. Two of these CpG sites were selected by their discriminatory power in 258 DNAm profiles – they were either methylated in pluripotent or non-pluripotent cells. The difference between these two β-values provides an Epi-Pluri-Score that was validated on independent DNAm-datasets (264 pluripotent and 1,951 non-pluripotent samples) with 99.9% specificity and 98.9% sensitivity. This score was complemented by a third CpG within the gene POU5F1 (OCT4), which better demarcates early differentiation events. We established pyrosequencing assays for the three relevant CpG sites and thereby correctly classified DNA of 12 pluripotent cell lines and 31 non-pluripotent cell lines. Furthermore, DNAm changes at these three CpGs were tracked in the course of differentiation of iPSCs towards mesenchymal stromal cells. The Epi-Pluri-Score does not give information on lineage-specific differentiation potential, but it provides a simple, reliable and robust biomarker to support high-throughput classification into either pluripotent or non-pluripotent cells.
Coherent control of optical polarization effects in metamaterials
Authors: Mousavi Seyedmohammad A. , Plum Eric , Shi Jinhui , Zheludev Nikolay I. 
Published: March 2015

AbstractProcessing of photonic information usually relies on electronics. Aiming to avoid the conversion between photonic and electronic signals, modulation of light with light based on optical nonlinearity has become a major research field and coherent optical effects on the nanoscale are emerging as new means of handling and distributing signals. Here we demonstrate that in slabs of linear material of sub-wavelength thickness optical manifestations of birefringence and optical activity (linear and circular birefringence and dichroism) can be controlled by a wave coherent with the wave probing the polarization effect. We demonstrate this in proof-of-principle experiments for chiral and anisotropic microwave metamaterials, where we show that the large parameter space of polarization characteristics may be accessed at will by coherent control. Such control can be exerted at arbitrarily low intensities, thus arguably allowing for fast handling of electromagnetic signals without facing thermal management and energy challenges.
Folic acid supplementation improves microvascular function in older adults through nitric oxide-dependent mechanisms
Authors: Stanhewicz Anna E. , Alexander Lacy M. , Kenney W. Larry 
Published: March 2015

Older adults have reduced vascular endothelial function, evidenced by attenuated nitric oxide (NO)-dependent cutaneous vasodilatation. Folic acid and its metabolite, 5-methyltetrahydrofolate (5-MTHF), are reported to improve vessel function. We hypothesized that (i) local 5-MTHF administration and (ii) chronic folic acid supplementation would improve cutaneous microvascular function in ageing through NO-dependent mechanisms. There were two separate studies in which there were 11 young (Y: 22±1 years) and 11 older (O: 71±3 years) participants. In both studies, two intradermal microdialysis fibres were placed in the forearm skin for local delivery of lactated Ringer's solution with or without 5 mM 5-MTHF. Red cell flux was measured by laser-Doppler flowmetry. Cutaneous vascular conductance [CVC=red cell flux/mean arterial pressure] was normalized as percentage maximum CVC (%CVCmax) (28 mM sodium nitroprusside, local temperature 43°C). In study 1 after CVC plateaued during local heating, 20 mM NG-nitro-L-arginine methyl ester (L-NAME) was perfused at each site to quantify NO-dependent vasodilatation. The local heating plateau (%CVCmax: O=82±3 vs Y=96±1, P=0.002) and NO-dependent vasodilatation (%CVCmax: O=26±6% vs Y=49±5, P=0.03) were attenuated in older participants. 5-MTHF augmented the overall (%CVCmax=91±2, P=0.03) and NO-dependent (%CVCmax=43±9%, P=0.04) vasodilatation in older but not young participants. In study 2 the participants ingested folic acid (5 mg/day) or placebo for 6 weeks in a randomized, double-blind, crossover design. A rise in oral temperature of 1°C was induced using a water-perfused suit, body temperature was held and 20 mM L-NAME was perfused at each site. Older participants had attenuated reflex (%CVCmax: O=31±8 vs Y=44±5, P=0.001) and NO-dependent (%CVCmax: O=9±2 vs Y=21±2, P=0.003) vasodilatation. Folic acid increased CVC (%CVCmax=47±5%, P=0.001) and NO-dependent vasodilatation (20±3%, P=0.003) in the older but not the young participants. Both local perfusion of 5-MTHF and supplementation with folic acid increase vasodilatation in ageing individuals through NO-dependent mechanisms.
Probabilistic generation of time‐coupled aggregate residential demand patterns
Authors: Sajjad Intisar Ali , Chicco Gianfranco , Napoli Roberto 
Published: March 2015

For distribution system studies, a relevant aspect is the characterisation of the aggregate demand in a feeder. The probabilistic model of the aggregate demand is very useful for system operators or aggregators to extract information about the demand side behaviour in the operation of smart grids and microgrids. The time step used to scan the aggregate demand pattern is very important to preserve the information about the consumers’ behaviour and the related uncertainty. The conventional models of aggregate electrical demand consider an average value for a specific time step (e.g. 30 min to 1 h). In this study, a faster time step (1 min) is considered to construct a time‐coupled probabilistic model of the aggregate residential demand based on Beta distributions. For a given number of aggregate loads, the parameters of the Beta distributions are found by taking into account the aggregate demand pattern variations at two successive time steps. The probabilistic model is then used to generate a number of aggregate demand scenarios. The effectiveness of the proposed scenario generation method is evaluated by using goodness of fit tests such as the Kolmogorov–Smirnov test and the average mean absolute percentage error.
Recombination in diverse maize is stable, predictable, and associated with genetic load
Authors: Rodgers-Melnick Eli , Bradbury Peter J. , Elshire Robert J. , Glaubitz Jeffrey C. , Acharya Charlotte B. , Mitchell Sharon E. , Li Chunhui , Li Yongxiang , Buckler Edward S. 
Published: March 2015

Significance
Meiotic recombination is known to vary over 1,000-fold in many eukaryotic organisms, including maize. This regional genomic variation has enormous consequences for plant breeders, who rely on meiotic cross-overs to fine-map quantitative traits and introgress favorable alleles. Deleterious mutations are also predicted to accumulate preferentially within low-recombination regions, particularly within historically outcrossing species, such as maize. Here, we show that meiotic recombination is predictable across diverse crosses based on several genomic features of the reference genome. We demonstrate that the extant patterns of recombination are historically stable and tied to variation in the number of deleterious mutations. The ability of plant breeders to exploit recombination to purge segregating deleterious alleles will determine the efficacy of future crop improvement.
Permafrost carbon−climate feedback is sensitive to deep soil carbon decomposability but not deep soil nitrogen dynamics
Authors: Koven Charles D. , Lawrence David M. , Riley William J. 
Published: March 2015

Significance
As the climate warms, the carbon balance of arctic ecosystems will respond in two opposing ways: Plants will grow faster, leading to a carbon sink, while thawing permafrost will lead to decomposition and loss of soil carbon. However, thawing permafrost also releases nitrogen that fertilizes plant growth, offsetting some carbon losses. The balance of these processes determines whether these ecosystems will act as a stabilizing or destabilizing feedback to climate change. We show that this balance is determined by the rate at which permafrost carbon decomposes as it thaws, and that the stabilizing effects of nitrogen from permafrost is weaker than the destabilizing carbon losses from those soil layers.
Functionally conserved architecture of hepatitis C virus RNA genomes
Authors: Mauger David M. , Golden Michael , Yamane Daisuke , Williford Sara , Lemon Stanley M. , Martin Darren P. , Weeks Kevin M. 
Published: March 2015

Significance
Plus-sense RNA viruses cause diverse pathologies in humans. Viral RNA genomes are selected to encode information both in their primary sequences and in their higher-order tertiary structures required to replicate and to evade host immune responses. We interrogated the physical structures of three evolutionarily divergent hepatitis C virus (HCV) RNA genomes using high-throughput chemical probing and found, along with all previously known RNA-structure–based regulatory elements, diverse previously uncharacterized structures that impact viral replication. We also characterized strategies by which the HCV genomic RNA structure masks detection by innate immune sensors. This structure-first strategy for comparative analysis of genome-wide RNA structure can be broadly applied to understand the contributions of higher-order genome structure to viral replication and pathogenicity.