bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural Evolution of Chemically-Driven RuO2 Nanowires and 3-Dimensional Design for Photo-Catalytic Applications
Authors: Park Joonmo , Lee Jae Won , Ye Byeong Uk , Chun Sung Hee , Joo Sang Hoon , Park Hyunwoong , Lee Heon , Jeong Hu Young , Kim Myung Hwa , Baik Jeong Min 
Published: July 2015

AbstractGrowth mechanism of chemically-driven RuO2 nanowires is explored and used to fabricate three-dimensional RuO2 branched Au-TiO2 nanowire electrodes for the photostable solar water oxidation. For the real time structural evolution during the nanowire growth, the amorphous RuO2 precursors (Ru(OH)3·H2O) are heated at 180 °C, producing the RuO2 nanoparticles with the tetragonal crystallographic structure and Ru enriched amorphous phases, observed through the in-situ synchrotron x-ray diffraction and the high-resolution transmission electron microscope images. Growth then proceeds by Ru diffusion to the nanoparticles, followed by the diffusion to the growing surface of the nanowire in oxygen ambient, supported by the nucleation theory. The RuO2 branched Au-TiO2 nanowire arrays shows a remarkable enhancement in the photocurrent density by approximately 60% and 200%, in the UV-visible and Visible region, respectively, compared with pristine TiO2 nanowires. Furthermore, there is no significant decrease in the device’s photoconductance with UV-visible illumination during 1 day, making it possible to produce oxygen gas without the loss of the photoactvity.
Two short sequences in OsNAR2.1 promoter are necessary for fully activating the nitrate induced gene expression in rice roots
Authors: Liu Xiaoqin , Feng Huimin , Huang Daimin , Song Miaoquan , Fan Xiaorong , Xu Guohua 
Published: July 2015

AbstractNitrate is an essential nitrogen source and serves as a signal to control growth and gene expression in plants. In rice, OsNAR2.1 is an essential partner of multiple OsNRT2 nitrate transporters for nitrate uptake over low and high concentration range. Previously, we have reported that −311 bp upstream fragment from the translational start site in the promoter of OsNAR2.1 gene is the nitrate responsive region. To identify the cis-acting DNA elements necessary for nitrate induced gene expression, we detected the expression of beta-glucuronidase (GUS) reporter in the transgenic rice driven by the OsNAR2.1 promoter with different lengths and site mutations of the 311 bp region. We found that −129 to −1 bp region is necessary for the nitrate-induced full activation of OsNAR2.1. Besides, the site mutations showed that the 20 bp fragment between −191 and −172 bp contains an enhancer binding site necessary to fully drive the OsNAR2.1 expression. Part of the 20 bp fragment is commonly presented in the sequences of different promoters of both the nitrate induced NAR2 genes and nitrite reductase NIR1 genes from various higher plants. These findings thus reveal the presence of conserved cis-acting element for mediating nitrate responses in plants.
Maskless Lithography and in situ Visualization of Conductivity of Graphene using Helium Ion Microscopy
Authors: Iberi Vighter , Vlassiouk Ivan , Zhang X.-G. , Matola Brad , Linn Allison , Joy David C. , Rondinone Adam J. 
Published: July 2015

AbstractThe remarkable mechanical and electronic properties of graphene make it an ideal candidate for next generation nanoelectronics. With the recent development of commercial-level single-crystal graphene layers, the potential for manufacturing household graphene-based devices has improved, but significant challenges still remain with regards to patterning the graphene into devices. In the case of graphene supported on a substrate, traditional nanofabrication techniques such as e-beam lithography (EBL) are often used in fabricating graphene nanoribbons but the multi-step processes they require can result in contamination of the graphene with resists and solvents. In this letter, we report the utility of scanning helium ion lithography for fabricating functional graphene nanoconductors that are supported directly on a silicon dioxide layer and we measure the minimum feature size achievable due to limitations imposed by thermal fluctuations and ion scattering during the milling process. Further we demonstrate that ion beams, due to their positive charging nature, may be used to observe and test the conductivity of graphene-based nanoelectronic devices in situ.
Metabonomic analysis of potential biomarkers and drug targets involved in diabetic nephropathy mice
Authors: Wei Tingting , Zhao Liangcai , Jia Jianmin , Xia Huanhuan , Du Yao , Lin Qiuting , Lin Xiaodong , Ye Xinjian , Yan Zhihan , Gao Hongchang 
Published: July 2015

AbstractDiabetic nephropathy (DN) is one of the lethal manifestations of diabetic systemic microvascular disease. Elucidation of characteristic metabolic alterations during diabetic progression is critical to understand its pathogenesis and identify potential biomarkers and drug targets involved in the disease. In this study, 1H nuclear magnetic resonance (1H NMR)-based metabonomics with correlative analysis was performed to study the characteristic metabolites, as well as the related pathways in urine and kidney samples of db/db diabetic mice, compared with age-matched wildtype mice. The time trajectory plot of db/db mice revealed alterations, in an age-dependent manner, in urinary metabolic profiles along with progression of renal damage and dysfunction. Age-dependent and correlated metabolite analysis identified that cis-aconitate and allantoin could serve as biomarkers for the diagnosis of DN. Further correlative analysis revealed that the enzymes dimethylarginine dimethylaminohydrolase (DDAH), guanosine triphosphate cyclohydrolase I (GTPCH I) and 3-hydroxy-3-methylglutaryl-CoA lyase (HMG-CoA lyase) were involved in dimethylamine metabolism, ketogenesis and GTP metabolism pathways, respectively and could be potential therapeutic targets for DN. Our results highlight that metabonomic analysis can be used as a tool to identify potential biomarkers and novel therapeutic targets to gain a better understanding of the mechanisms underlying the initiation and progression of diseases.
Serum pro-BDNF/BDNF as a treatment biomarker for response to docosahexaenoic acid in traumatized people vulnerable to developing psychological distress: a randomized controlled trial
Authors: Matsuoka Y , Nishi D , Tanima Y , Itakura M , Kojima M , Hamazaki K , Noguchi H , Hamazaki T 
Published: July 2015

AbstractOur open-label pilot study showed that supplementation with docosahexaenoic acid (DHA) increased serum brain-derived neurotrophic factor (BDNF) levels and that there might be an association between changes in serum BDNF levels and reduced psychological distress. Animal research has indicated that a DHA-enriched diet increases BDNF in the brain. In this randomized double-blind controlled trial of severely injured patients vulnerable to posttraumatic stress disorder (PTSD) and depression, we examined whether DHA increases serum BDNF levels and whether changes in BDNF levels are associated with subsequent symptoms of PTSD and depression. Patients received 1470 mg per day of DHA plus 147 mg per day of eicosapentaenoic acid (EPA; n=53) or placebo (n=57) for 12 weeks. Serum levels of mature BDNF and precursor pro-BDNF at baseline and 12-week follow-up were measured using enzyme-linked immunosorbent assay kits. At 12 weeks, we used the Clinician-Administered PTSD Scale to assess PTSD symptoms and depressive symptoms by the Montgomery–Åsberg Depression Rating Scale. We found a significant increase in serum BDNF levels during the trial in the DHA and placebo groups with no interaction between time and group. Changes in BDNF levels were not associated with PTSD severity but negatively associated with depression severity (Spearman’s ρ=−0.257, P=0.012). Changes in pro-BDNF were also negatively associated with depression severity (Spearman’s ρ=−0.253, P=0.013). We found no specific effects of DHA on increased serum levels of BDNF and pro-BDNF; however, evidence in this study suggests that increased BDNF and pro-BDNF have a protective effect by minimizing depression severity.
Stochastic game dynamics under demographic fluctuations
Authors: Huang Weini , Hauert Christoph , Traulsen Arne 
Published: July 2015

Significance
This contribution breaks with the tradition to restrict stochastic evolutionary game dynamics to populations of constant size and introduces a theoretical framework to investigate relevant and natural changes arising in populations that vary in size according to fitness—a feature common to many real biological systems. Explicitly including ecological variation can result in significant effects on the stochastic evolutionary trajectories while providing a transparent link to the established, deterministic Lotka–Volterra systems.
Behavioral consequences of selective damage to frontal pole and posterior cingulate cortices
Authors: Mansouri Farshad A. , Buckley Mark J. , Mahboubi Majid , Tanaka Keiji 
Published: July 2015

Significance
Frontal pole cortex (FPC) refers to the most anterior part of prefrontal cortex, a region that is highly developed in anthropoid primates. However, because of technical difficulties in studying this area, its role in primate cognition had remained largely unknown. We studied effects of selective bilateral lesions within FPC on monkeys’ cognitive flexibility. FPC lesion did not impair the performance in well-learned cognitively demanding tasks. However, FPC-lesioned monkeys remained more focused than control monkeys in exploiting the current task when they faced newly introduced interruptions by a simple secondary task or free rewards. This unique pattern of behavioral changes in FPC-lesioned monkeys suggests that FPC is involved in redistribution of cognitive resources from the current task to novel opportunities.
Tracing the ingredients for a habitable earth from interstellar space through planet formation
Authors: Bergin Edwin A. , Blake Geoffrey A. , Ciesla Fred , Hirschmann Marc M. , Li Jie 
Published: July 2015

SignificanceWith the rapid pace at which exoplanets are being discovered, many efforts have now been dedicated to identifying which planets are expected to have the ingredients necessary for the development of life. In this work we explore the relative disposition of the essential elements carbon and nitrogen in each stage of star and planet formation, using the Earth and our solar system as grounding data. Our results suggest that planets like the Earth are readily supplied with these key elements, but their relative amounts on the surface and in the atmosphere will be highly variable.
Limits and patterns of cytomegalovirus genomic diversity in humans
Authors: Renzette Nicholas , Pokalyuk Cornelia , Gibson Laura , Bhattacharjee Bornali , Schleiss Mark R. , Hamprecht Klaus , Yamamoto Aparecida Y. , Mussi-Pinhata Marisa M. , Britt William J. , Jensen Jeffrey D. , Kowalik Timothy F. 
Published: July 2015

Significance
Human cytomegalovirus (HCMV) is the leading cause of birth defects associated with infections and a leading cause of transplantation failure. This study reveals the patterns and limits of HCMV genomic diversity by performing a large-scale analysis of HCMV sequences sampled from human hosts, identifying the hot and cold spots of variability. We find that the diversity is unevenly distributed across three host compartments and show that HCMV populations of vascular compartments are genetically constrained while enriched for polymorphisms of glycoproteins and regulatory proteins. This work significantly advances our understanding of the genomic diversity of HCMV in humans and has clear implications for the development of therapeutics against HCMV.
Skip residues modulate the structural properties of the myosin rod and guide thick filament assembly
Authors: Taylor Keenan C. , Buvoli Massimo , Korkmaz Elif Nihal , Buvoli Ada , Zheng Yuqing , Heinze Nathan T. , Cui Qiang , Leinwand Leslie A. , Rayment Ivan 
Published: July 2015

Significance
Myosins are cellular motors that promote muscle contraction by converting chemical energy into mechanical force. The myosin molecule self-assembles through its coiled-coil rod domain into the highly ordered thick filaments of the sarcomeres, which represent the basic contractile unit of the muscle. Because there is limited information about the mechanisms of filament formation, and mutations in the rod domain cause muscle disease, we investigated the molecular properties and function of four regions of the rod containing an extra amino acid (skip residue) predicted to alter the regular organization of the coiled-coil. To our knowledge, this is the first study reporting that these regions fold into specialized structures engaged in promoting proper myosin assembly into the thick filaments.
Molecular basis for the specific recognition of the metazoan cyclic GMP-AMP by the innate immune adaptor protein STING
Authors: Shi Heping , Wu Jiaxi , Chen Zhijian J. , Chen Chuo 
Published: July 2015

Significance
The presence of cytosolic DNA in mammalian cells signifies microbial invasions and triggers the DNA sensor protein cGAS to produce the second messenger molecule 2′3′-cGAMP, which elicits innate immune responses by binding to and activating the homodimerized adaptor protein STING. Here we show that the high affinity of the asymmetric ligand 2′3′-cGAMP to the symmetric dimer of STING originates from its unique mixed phosphodiester linkages. 2′3′-cGAMP, but not its linkage isomers, adopts an organized free-ligand conformation that resembles the STING-bound conformation and pays low energy costs in changing into the active conformation. Whereas biological structural studies have focused on analyses of protein conformations, our results demonstrate that analyses of free-ligand conformations can be equally important in understanding protein–ligand interactions.
Structure of a herpesvirus nuclear egress complex subunit reveals an interaction groove that is essential for viral replication
Authors: Leigh Kendra E. , Sharma Mayuri , Mansueto My Sam , Boeszoermenyi Andras , Filman David J. , Hogle James M. , Wagner Gerhard , Coen Donald M. , Arthanari Haribabu 
Published: July 2015

SignificanceHuman cytomegalovirus (HCMV) is an important human pathogen. Current anti-HCMV therapies suffer from toxicities, drug resistance, and/or pharmacokinetic limitations. A possible antiviral drug target is a two-subunit complex that orchestrates nuclear egress, an essential, unusual mechanism by which nucleocapsids move from the nucleus to the cytoplasm during viral replication. We solved the structure of the conserved core of one subunit of the complex, mapped the primary interaction interface with the other subunit, and tested the importance of specific residues for subunit interactions and viral replication. The combined biophysical and biological analyses presented here develop molecular understanding of nuclear egress and identify a groove that includes a large cavity on the subunit as an attractive target for yet to be identified inhibitors.
Chloroplasts extend stromules independently and in response to internal redox signals
Authors: Brunkard Jacob O. , Runkel Anne M. , Zambryski Patricia C. 
Published: July 2015

SignificanceChloroplasts are critical, dynamic organelles in plant cells responsible for photosynthesis and myriad other aspects of metabolism. In recent years, plant cell biologists have increasingly focused on the formation of thin, long extensions from plastids called “stromules.” Although stromules have been observed in all land plant species and cell types investigated, we do not know why these projections form or what they do. Here we demonstrate that stromules form in response to light-related redox signals inside the chloroplast. We then show that chloroplasts extracted from plant cells can make stromules independently. These discoveries suggest that stromules may be involved in transmitting signals from within the chloroplast to other subcellular compartments.
DINGO: differential network analysis in genomics
Authors: Ha Min Jin , Baladandayuthapani Veerabhadran , Do Kim-Anh 
Published: July 2015

AbstractMotivation: Cancer progression and development are initiated by aberrations in various molecular networks through coordinated changes across multiple genes and pathways. It is important to understand how these networks change under different stress conditions and/or patient-specific groups to infer differential patterns of activation and inhibition. Existing methods are limited to correlation networks that are independently estimated from separate group-specific data and without due consideration of relationships that are conserved across multiple groups.Method: We propose a pathway-based differential network analysis in genomics (DINGO) model for estimating group-specific networks and making inference on the differential networks. DINGO jointly estimates the group-specific conditional dependencies by decomposing them into global and group-specific components. The delineation of these components allows for a more refined picture of the major driver and passenger events in the elucidation of cancer progression and development.Results: Simulation studies demonstrate that DINGO provides more accurate group-specific conditional dependencies than achieved by using separate estimation approaches. We apply DINGO to key signaling pathways in glioblastoma to build differential networks for long-term survivors and short-term survivors in The Cancer Genome Atlas. The hub genes found by mRNA expression, DNA copy number, methylation and microRNA expression reveal several important roles in glioblastoma progression.Availability and implementation: R Package at: odin.mdacc.tmc.edu/∼vbaladan.Contact: veera@mdanderson.orgSupplementary information: Supplementary data are available at Bioinformatics online.
Invasive Fusariosis in the Voriconazole Era: Single-Center 13-Year Experience
Authors: Stempel Jessica M. , Hammond Sarah P. , Sutton Deanna A. , Weiser Linda M. , Marty Francisco M. 
Published: July 2015

Abstract
Background.  Invasive fusariosis remains an aggressive, albeit infrequent infection in immunocompromised patients.
Methods.  We identified all cases of invasive fusariosis between January 2002 and December 2014. We recorded patient characteristics including clinical presentation, treatment, and outcomes at 6 and 12 weeks after diagnosis, as well as species identification and antifungal drug susceptibilities.
Results.  Fifteen patients were diagnosed with proven (12, 80%) or probable (3, 20%) fusariosis. Median age was 60 years (range, 26–78), and 10 patients were male. Underlying conditions included hematological malignancies (13, 87%), juvenile idiopathic arthritis (1, 7%), and third-degree burns (1, 7%). Five patients underwent hematopoietic stem-cell transplantation before diagnosis. Six patients (40%) received systemic glucocorticoids, and 11 patients (73%) had prolonged neutropenia at the time of diagnosis. Clinical presentations included the following: skin/soft tissue infection (8, 53%), febrile neutropenia (4, 27%), respiratory tract infection (2, 13%), and septic arthritis (1, 7%). Twelve patients were treated with voriconazole: 6 (40%) with voriconazole alone, 4 (27%) with voriconazole and terbinafine, and 2 (13%) with voriconazole, terbinafine, and amphotericin. One patient (7%) was treated with terbinafine alone, and another with micafungin alone. Four patients underwent surgical debridement (4, 27%). Susceptibility testing was performed on 9 isolates; 8 demonstrated voriconazole minimum inhibitory concentrations ≥4 µg/mL. The cumulative probability of survival was 66.7% and 53.3% at 6 and 12 weeks after diagnosis.
Conclusions.  Mortality associated with invasive fusariosis remains high. Cumulative mortality at our center was lower than previous reports despite elevated voriconazole minimum inhibitory concentrations. Combination therapy should be studied systematically for fusariosis.
The Role of Recombination in Evolutionary Rescue
Authors: Uecker Hildegard , Hermisson Joachim 
Published: July 2015

AbstractHow likely is it that a population escapes extinction through adaptive evolution? The answer to this question is of great relevance in conservation biology, where we aim at species’ rescue and the maintenance of biodiversity, and in agriculture and epidemiology, where we seek to hamper the emergence of pesticide or drug resistance. By reshuffling the genome, recombination has two antagonistic effects on the probability of evolutionary rescue: it generates and it breaks up favorable gene combinations. Which of the two effects prevails, depends on the fitness effects of mutations and on the impact of stochasticity on the allele frequencies. In this paper, we analyze a mathematical model for rescue after a sudden environmental change when adaptation is contingent on mutations at two loci. The analysis reveals a complex nonlinear dependence of population survival on recombination. We moreover find that, counterintuitively, a fast eradication of the wildtype can promote rescue in the presence of recombination. The model also shows that two-step rescue is not unlikely to happen and can even be more likely than single-step rescue (where adaptation relies on a single mutation), depending on the circumstances.
A New Method to Detect Event-Related Potentials Based on Pearson’s Correlation
Authors: Giroldini William , Pederzoli Luciano , Bilucaglia Marco , Melloni Simone , Tressoldi Patrizio 
Published: July 2015

AbstractEvent-Related Potentials (ERPs) are widely used in Brain-Computer Interface applications and in neuroscience.Normal EEG activity is rich in background noise and therefore, in order to detect ERPs, it is usually necessary to take the average from multiple trials to reduce the effects of this noise.The noise produced by EEG activity itself is not correlated with the ERP waveform and so, by calculating the average, the noise is decreased by a factor inversely proportional to the square root of N, where N is the number of averaged epochs.This is the easiest strategy currently used to detect ERPs, which is based on calculating the average of each ERP’s waveform, these waveforms being time-and phase-locked.In this paper a new method called GW6 is proposed, which calculates the ERP using a mathematical method based only on Pearson's Correlation.This results in a graph with the same time resolution as the classical ERP and which contains only positive peaks representing the increase -in consonance to the stimuli - in EEG signal correlation over all channels.This new method is also useful for selectively identifying and highlighting any hidden components of the ERP response that are not phase-locked, and that are usually hidden in the standard and simple method based on the averaging of all the epochs.These hidden components seem to be caused by variations (between each successive stimulus) of the ERP's inherent phase latency period (jitter), although the same stimulus across all EEG channels produces a reasonably constant phase.For this reason, this new method could be very helpful to investigate these hidden components of the ERP response and to develop applications for scientific and medical purposes.Moreover, this new method is more resistant to EEG artifacts than the standard calculations of the average.The method we are proposing can be directly used in the form of a process written in the well known Matlab programming language and can be easily and quickly written in any other software language.