bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adaptive trimmed t‐statistics for identifying predominantly high expression in a microarray experiment
Authors: Gleiss Andreas , Sanchez‐Cabo Fatima , Perco Paul , Tong Dan , Heinze Georg 
Published: October 2010

AbstractOften, interesting candidate tumor markers are not only genes that show homogeneously higher expression (HHE) in tumor samples compared to control samples, but also genes with only predominantly higher expression (PHE), i.e. genes which exhibit higher expression in at least 80 per cent of tumor samples. Standard parametric test statistics used in the analysis of microarray experiments may fail with PHE as a consequence of the mixture of distributions present in the tumor group. As alternative we consider trimmed t‐statistics which compare group mean values after removing outliers in each group. The trimming proportion can be chosen adaptively, either based on a boxplot outlier detection rule or by optimization over a series of tests with varying trimming proportions. The trimmed t‐statistics can be plugged into the ‘significance analysis of microarrays’ (SAM) procedure, yielding the modified boxplot rule test (modBox) and the modified optimization test (modOpt), respectively. By means of simulation of microarray experiments, we show that modOpt is superior to contenders in detecting PHE, while there is only little loss in efficiency under HHE compared to SAM. Analysis of a real microarray experiment revealed that, out of nearly 29 000 genes, about 417 genes exhibiting PHE are detected by modOpt but missed by SAM. Copyright © 2010 John Wiley & Sons, Ltd.
Heteroepitaxial Growth of Core–Shell and Core–Multishell Nanocrystals Composed of Palladium and Gold
Authors: Wang Feng , Sun Ling‐Dong , Feng Wei , Chen Huanjun , Yeung Man Hau , Wang Jianfang , Yan Chun‐Hua 
Published: October 2010

AbstractThe heteroepitaxial growth of the core–shell nanocrystals composed of Pd and Au is developed. Pd nanocubes or Au nano‐octahedrons are utilized as the cores. The growths of the Au and Pd shells are realized under similar conditions, where the same reducing agent and stabilizing surfactant are employed. The preparation is highly controllable, and the epitaxial growth is repeated up to three times to yield Pd@Au@Pd@Au and Au@Pd@Au@Pd core–trishell nanocrystals. The thickness of each shell is readily varied by changing the amount of the metal salts used for growth. All of the nanocrystal products have narrow size distributions and are single crystalline. The plasmon resonance properties of these nanocrystals are mainly determined by the exterior shell. The plasmon of the Pd‐shell‐terminated nanocrystals is suppressed, while that of the Au‐shell‐terminated ones is recovered and is stronger when the Au shell becomes thicker. This growth method can potentially be extended to other metals for the synthetic design of more complex core–multishell metal nanostructures with desirable optical, catalytic, and magnetic properties.
Transition Voltage Spectroscopy of Porphyrin Molecular Wires
Authors: Bennett Neil , Xu Gengzhao , Esdaile Louisa J. , Anderson Harry L. , Macdonald J. Emyr , Elliott Martin 
Published: October 2010

AbstractMeasurements are presented of the current‐voltage (I–V) characteristics of individual thiol‐tethered porphyrin molecules (isolated in an alkanethiol matrix) and of self‐assembled monolayers. In both cases, it is found that I/V2 displays a minimum at a characteristic “transition voltage” Vm. Repeated measurements of the transition voltage enable both its time development and statistical behavior to be determined. For isolated molecules, the transition voltage shows a multipeaked distribution of values, indicating the presence of a small number of distinct molecular/contact configurations, each having different transport characteristics. For self‐assembled monolayers, in contrast, a single‐peaked distribution was observed, which is consistent with parallel conduction through many molecules.
Preweaning Mn exposure leads to prolonged astrocyte activation and lasting effects on the dopaminergic system in adult male rats
Authors: Kern Cynthia H. , Smith Donald R. 
Published: October 2010

AbstractLittle is known about the effects of manganese (Mn) exposure over neurodevelopment and whether these early insults result in effects lasting into adulthood. To determine if early Mn exposure produces lasting neurobehavioral and neurochemical effects, we treated neonate rats with oral Mn (0, 25, or 50 mg Mn/kg/d over PND 1–21) and evaluated (1) behavioral performance in the open arena in the absence (PND 97) and presence (PND 98) of a d‐amphetamine challenge, (2) brain dopamine D1 and D2‐like receptors and dopamine transporter densities in the prefrontal cortex, striatum, and nucleus accumbens (PND 107), and (3) astrocyte marker glial fibrillary acidic protein (GFAP) levels in these same brain regions (PND 24 and 107). We found that preweaning Mn exposure did not alter locomotor activity or behavior disinhibition in adult rats, though Mn‐exposed animals did exhibit an enhanced locomotor response to d‐amphetamine challenge. Preweaning Mn exposure led to increased D1 and D2 receptor levels in the nucleus accumbens and prefrontal cortex, respectively, compared with controls. We also found increased GFAP expression in the prefrontal cortex in Mn‐exposed PND 24 weanlings, and increased GFAP levels in prefrontal cortex, medial striatum and nucleus accumbens of adult (PND 107) rats exposed to preweaning Mn, indicating an effect of Mn exposure on astrogliosis that persisted and/or progressed to other brain regions in adult animals. These data show that preweaning Mn exposure leads to lasting molecular and functional impacts in multiple brain regions of adult animals, long after brain Mn levels returned to normal. Synapse, 2011. © 2010 Wiley‐Liss, Inc.
Vitamin C protects against ethanol and PTZ‐induced apoptotic neurodegeneration in prenatal rat hippocampal neurons
Authors: Naseer M.I. , Ullah N. , Ullah I. , Koh P.O. , Lee H.Y. , Park M.S. , Kim M.O. 
Published: October 2010

AbstractExposure to alcohol during brain development may cause a neurological syndrome called fetal alcohol syndrome, characterized by pre‐ and postnatal growth deficiencies, craniofacial anomalies, and evidence of CNS dysfunction. The objective of this study was to evaluate pentylenetetrazol (PTZ) and ethanol effects on Bax, Bcl‐2 expression, which further induced activation of caspase‐3, release of cytochrome‐c from mitochondria, and to observe the protective effects of vitamin C (vit‐C) against PTZ and ethanol‐induced apoptotic neurodegeneration in primary‐cultured neuronal cells at gestational day 17.5. Apoptotic neurodegeneration and neuroprotective effect of vit‐C were measured by using 3‐[4,5‐dimethylthiazol‐2‐yl]‐2,5‐diphenly tetrazolium bromide assay, Western blot analysis, which further conformed by the measurement of mitochondrial membrane potential using JC‐1 detection kit and immunofluorescence analysis. The results showed that PTZ and ethanol produced extensive Bax‐dependent caspase‐9 and caspase‐3 activation and caused neuronal apoptosis. Furthermore, the cotreatment of vit‐C along with ethanol and PTZ showed significantly decreased expression of Bax, caspase‐9, caspase‐3, cytochrome‐c, and significantly increased expression of antiapoptotic Bcl‐2 protein when compared with control group. Our findings indicate that PTZ and ethanol activate an intrinsic apoptotic death program in neurons that is likely to contribute to the neuropathologic effects in fetal alcohol exposure, and vit‐C can prevent some of the deleterious effects of PTZ and ethanol on the developing brain. The available experimental evidence and the safety of vit‐C in pregnancy suggest the experimental use of ascorbic acid as a new and effective protective agent ethanol and PTZ‐induced apoptotic neurodegeneration. Synapse, 2011. © 2010 Wiley‐Liss, Inc.
Discrimination of n‐3 Rich Oils by Gas Chromatography
Authors: Araujo Pedro , Zeng Yingxu , Du Zhen‐Yu , Nguyen Thu‐Thao , Frøyland Livar , Grung Bjørn 
Published: October 2010

AbstractExploring the capabilities of instrumental techniques for discriminating n‐3 rich oils derived from animals is a very important though much neglected area that was emphasized more than 100 years ago. In this study the potential of gas chromatography (GC) for discriminating full fatty acid methyl ester (FAME) profiles from fish (cod liver and salmon) and marine mammal (seal and whale) oils is evaluated by means of principal component analysis (PCA). The FAME profiles from plant oils such as rapeseed, linseed and soy oils and seven different brands of n‐3 supplements are also used in the discrimination process. The results from the PCA plots can reliably distinguish between plant, n‐3 supplements, fish and marine mammal oils. By removing the contribution of the n‐3 supplements and plant oils it is possible to discriminate between types of fish and marine animal oils. GC offers a rapid, simple and convenient means of discriminating oils from different species, brands and grades.
Lipid Classes and Fatty Acid Patterns are Altered in the Brain of γ‐Synuclein Null Mutant Mice
Authors: Guschina Irina , Millership Steve , O’Donnell Valerie , Ninkina Natalia , Harwood John , Buchman Vladimir 
Published: October 2010

AbstractThe well‐documented link between α‐synuclein and the pathology of common human neurodegenerative diseases has increased attention to the synuclein protein family. The involvement of α‐synuclein in lipid metabolism in both normal and diseased nervous system has been shown by many research groups. However, the possible involvement of γ‐synuclein, a closely‐related member of the synuclein family, in these processes has hardly been addressed. In this study, the effect of γ‐synuclein deficiency on the lipid composition and fatty acid patterns of individual lipids from two brain regions has been studied using a mouse model. The level of phosphatidylserine (PtdSer) was increased in the midbrain whereas no changes in the relative proportions of membrane polar lipids were observed in the cortex of γ‐synuclein‐deficient compared to wild‐type (WT) mice. In addition, higher levels of docosahexaenoic acid were found in PtdSer and phosphatidylethanolamine (PtdEtn) from the cerebral cortex of γ‐synuclein null mutant mice. These findings show that γ‐synuclein deficiency leads to alterations in the lipid profile in brain tissues and suggest that this protein, like α‐synuclein, might affect neuronal function via modulation of lipid metabolism.
Rice planting systems, global warming and outbreaks of Nilaparvata lugens (Stål)
Authors: Hu G. , Cheng X.N. , Qi G.J. , Wang F.Y. , Lu F. , Zhang X.X. , Zhai B.P. 
Published: October 2010

AbstractBrown Planthopper (BPH, Nilaparvata lugens (Stål)) is one of the most serious pests of rice in both temperate and tropical regions of East and South Asia and has become especially problematic over the past few years. In order to analyze the effect of the change of rice cropping system on the population dynamics of BPH, field surveys of the occurrence and distribution of BPH were performed and other relevant data, including light trap data and ovary dissection data were collected in nearly 40 Chinese counties encompassing six provinces (or municipalities), including Hainan, Guangxi, Anhui, Shanghai, Fujian and Guangdong from April to October in 2007.The mixed planting areas of single- and double-cropping rice in China include Hubei, South and Central Anhui, North Hunan, and North Jiangxi. In these areas, double-cropping rice has now been greatly reduced and single-cropping rice has been rapidly increasing since 1997. The surveys revealed that when the immigration peak of BPH occurred in June and July, the single-cropping rice was at the tillering to booting stage and fit for BPH, but early rice had already matured and most of late rice had not yet been transplanted. BPH immigrants from southern rice areas prefer to inhabit and breed in single-cropping rice paddies. Moreover, farming activities between early rice and late rice interrupted the continuous growth of BPH populations in double-cropping rice paddies. As a result, in comparison with data collected 30 years ago, the spatiotemporal dynamics and migration patterns of BPH have dramatically changed in the lower-middle reaches of the Yangtze River. In the mixed planting areas, due to their high suitability, the BPH population in single-cropping rice grew so quickly that it caused serious local damage and there was mass emigration of macropterous progeny to the Yangtze River Delta in late August and early September.Global warming may also affect BPH populations, where results suggest steadily warmer autumns have occurred from the 1990s on, with such conditions gradually the norm. The combination of ‘cooler summer’ and ‘warmer autumn’ are conditions known to promote outbreaks of BPH in the lower-middle reaches of the Yangtze River. Immigrant BPH arrivals in late August and September now cause serious damage to late-maturing mid-season rice and late rice in the lower-middle reaches of the Yangtze River.
A comparative assessment of the response of three fruit fly species (Diptera: Tephritidae) to a spinosad-based bait: effect of ammonium acetate, female age, and protein hunger
Authors: Piñero J.C. , Mau R.F.L. , Vargas R.I. 
Published: October 2010

AbstractAmmonia-releasing substances are known to play an important role in fruit fly (Diptera: Tephritidae) attraction to food sources, and this information has been exploited for the development of effective synthetic food-based lures and insecticidal baits. In field studies conducted in Hawaii, we examined the behavioural response of wild female oriental fruit fly (Bactrocera dorsalis(Hendel)), melon fly (B. cucurbitae(Coquillett)), and Mediterranean fruit fly (Ceratitis capitata(Wiedemann)) to spinosad-based GF-120 NF Naturalyte Fruit Fly Bait©formulated to contain either 0, 1 or 2% ammonium acetate. Use of visually-attractive yellow bait stations for bait application in the field allowed for proper comparisons among bait formulations. Field cage tests were also conducted to investigate, using a comparative behavioural approach, the effects of female age and protein starvation on the subsequent response of F1generationB. cucurbitaeandB. dorsalisto the same three bait formulations that were evaluated in the field. Our field results indicate a significant positive effect of the presence, regardless of amount, of AA in GF-120 forB. dorsalisandB. cucurbitae. ForC. capitata, there was a significant positive linear relationship between the relative amounts of AA in bait and female response. GF-120 with no AA was significantly more attractive to femaleC. capitata, but not to femaleB. dorsalisorB. cucurbitae,than the control treatment. Our field cage results indicate that the effects of varying amounts of AA present in GF-120 can be modulated by the physiological stage of the female flies and that the response of femaleB. cucurbitaeto GF-120 was consistently greater than that ofB. dorsalisover the various ages and levels of protein starvation regimes evaluated. Results are discussed in light of their applications for effective fruit fly suppression.
P300 deficits in adults with attention deficit hyperactivity disorder: a meta-analysis
Authors: Szuromi B. , Czobor P. , Komlósi S. , Bitter I. 
Published: October 2010

BackgroundThe P300 (P3) event-related potential (ERP) component, a possible endophenotype for attention deficit hyperactivity disorder (ADHD), has been widely examined in children, but received little attention in adults. Our objective was to conduct a meta-analysis of P3 studies in adults with ADHD.MethodWe searched the Medline and PsycINFO databases for controlled studies examining both adult ADHD and matched healthy controls. Six relevant publications were identified for the meta-analysis, which had comparable data across studies with regard to the amplitude of ERP components related to target detection (P3, P3b). Pooled effect size (ES) for P3 amplitude as well as the association of the ES with age and gender were investigated using meta-regression.ResultsComparing the ADHD group versus controls, the pooled effect size for a decrease in P3 amplitude was in the medium range (Cohen's d=−0.55, p=0.0006). Additionally, meta-regression revealed that decrease in P3 amplitude significantly varied with the mean age of ADHD patients (p=0.0087), with a gradual increasing of the difference at higher ages. Results also showed a significant association between the ES and gender, indicating a more pronounced reduction of P3 amplitude in the ADHD group versus controls when females were predominantly represented in the sample.ConclusionsTo our knowledge, this is the first meta-analysis of P3 characteristics in adults with ADHD. It reveals a significantly decreased P3 amplitude during target detection. Our result that the reduction in P3 amplitude increases with age is interpreted in a neurodevelopmental context.
Spontaneous confabulation, temporal context confusion and reality monitoring: A study of three patients with anterior communicating artery aneurysms
Authors: TURNER MARTHA S. , CIPOLOTTI LISA , SHALLICE TIM 
Published: October 2010

AbstractSpontaneous confabulation involves the production of false or distorted memories, and is commonly associated with ventromedial prefrontal damage. One influential theory proposes that the critical deficit is a failure to suppress currently irrelevant memory traces that intrude into ongoing thinking (Schnider & Ptak, 1999). In this study, we report experimental investigations with three spontaneously confabulating patients aimed at exploring this account. Using Schnider and Ptak’s (1999) continuous recognition paradigm, we replicated their experimental results with our patients. However, our data suggest that the critical impairment might be more generalized than a failure to suppress currently irrelevant memories. First, a temporal source monitoring task failed to show that previous memory traces intrude into the present. Second, a reality monitoring task revealed that confabulating patients had a tendency to misidentify imagined events as real, a result that cannot be explained in terms of temporal confusion. This error was specific to confabulating patients and was not shared by non-confabulating ACoA patients. Our data therefore suggest a more generalized impairment in source monitoring, not only on the basis of temporality or current relevance, but across a range of contextual domains, including information used to distinguish real memories from imaginings. (JINS, 2010, 16, 984–994.)
Development of a New Quantitative X-Ray Microanalysis Method for Electron Microscopy
Authors: Horny Paula , Lifshin Eric , Campbell Helen , Gauvin Raynald 
Published: October 2010

AbstractQuantitative X-ray microanalysis of thick samples is usually performed by measuring the characteristic X-ray intensities of each element in a sample and in corresponding standards. The ratio of the measured intensities from the unknown material to that from the standard is related to the concentration using the ZAF or ϕ(ρz) equations. Under optimal conditions, accuracies approaching 1% are possible. However, all the experimental conditions must remain the same during the sample and standard measurements. This is not possible with cold field emission scanning electron microscopes (FE-SEMs) where beam current can fluctuate around 5% in its stable regime. Very little work has been done on variable beam current conditions (Griffin, B.J. & Nockolds, C.E.,Scanning13, 307–312, 1991), and none relating to cold FE-SEM applications. To address this issue, a new method was developed using a single spectral measurement. It is similar in approach to the Cliff-Lorimer method developed for the analytical transmission electron microscope. However, corrections are made for X rays generated from thick specimens using the ratio of the characteristic X-ray intensities of two elements in the same material. The proposed method utilizes the ratio of the intensity of a characteristic X-ray normalized by the sum of X-ray intensities of all the elements measured for the sample, which should also reduce the amplitude of error propagation. Uncertainties in the physical parameters of X-ray generation are corrected using a calibration factor that must be previously acquired or calculated. As an example, when this method was applied to the calculation of the composition of Au-Cu National Institute of Standards and Technology standards measured with a cold field emission source SEM, relative accuracies better than 5% were obtained.
Streamlined Embedding of Cell Monolayers on Gridded Glass-Bottom Imaging Dishes for Correlative Light and Electron Microscopy
Authors: Hanson Hugo H. , Reilly James E. , Lee Rebecca , Janssen William G. , Phillips Greg R. 
Published: October 2010

AbstractCorrelative light and electron microscopy (CLEM) has facilitated study of intracellular trafficking. Routine application of CLEM would be advantageous for many laboratories but previously described techniques are particularly demanding, even for those with access to laser scanning confocal microscopy (LSCM) and transmission electron microscopy (TEM). We describe streamlined methods for TEM of green fluorescent protein (GFP)-labeled organelles after imaging by LSCM using gridded glass bottom imaging dishes. GFP-MAP 1A/1B LC3 (GFP-LC3) transfected cells were treated with rapamycin, fixed and imaged by LSCM. Confocal image stacks were acquired enabling full visualization of each GFP-LC3 labeled organelle. After LSCM, cells were embedded for TEM using a simplified two step method that stabilizes the glass bottom such that the block can be separated from the glass by mild heating. All imaging and TEM processing are performed in the same dish. The LSCM imaged cells were relocated on the block and serial sectioned. Correlation of LSCM, DIC, and TEM images was facilitated by cellular landmarks. All GFP labeled structures were successfully reidentified and imaged by serial section TEM. This method could make CLEM more accessible to nonspecialized laboratories with basic electron microscopy expertise and could be used routinely to confirm organelle localization of fluorescent puncta.
Bio2RDF: Convert, Provide And Reuse.
Authors: Nolin Marc-Alexandre , Corbeil Jacques , Lamontagne Luc , Dumontier Michel 
Published: October 2010

AbstractThe Bio2RDF project uses open-source Semantic Web technologies to provide interlinked life science data in order to maximize productivity and facilitate biological knowledge discovery. Using both syntactic and semantic data integration techniques, Bio2RDF puts into practice a simple methodology to generate and seamlessly integrate machine-interpretable data that can be powerfully interrogated with SPARQL-based queries to answer sophisticated questions.At its core, database records are converted into a set of statements or so-called triples that are captured together as a named graph annotated with provenance. The records and the entities they are about are provided with a Uniform Resource Identifier (URI) of the form http://bio2rdf.org/prefix:identifier, where the prefix indicates a reserved name for the dataset, record or terminological resource. The application of this simple method allows resources from over 40 datasets to integrate seamlessly at the syntactic level irrespective of whether the original data contains non-Bio2RDF URIs.However, when original data providers such as Uniprot provide their own RDF they will rightfully use URIs that resolve to their servers, but what should they do for externally defined entities? If they follow in Bio2RDF’s footsteps then every data provider will use a different URI. However, should original data providers present and implement a URI scheme, then it becomes possible for others to establish stable links to their resources. As such, we will witness the birth of a more stable linked data network, ensuring that data providers need not provide third party data in a redundant manner.