bluuebunny/crossref_metadata_2025 huggingface dataset:
Vertical distributions and relationships of cloud occurrence frequency as observed by MISR, AIRS, MODIS, OMI, CALIPSO, and CloudSat
Authors: Wu D. L. , Ackerman S. A. , Davies R. , Diner D. J. , Garay M. J. , Kahn B. H. , Maddux B. C. , Moroney C. M. , Stephens G. L. , Veefkind J. P. , Vaughan M. A.
Published: May 2009

Multi‐sensor cloud height observations are investigated and compared in terms of vertical and latitudinal distributions of monthly mean cloud occurrence frequency (COF). Although this study emphasizes the standard Multiangle Imaging SpectroRadiometer (MISR) cloud top height (CTH) retrieval, the strengths and weakness among different passive and active remote sensing techniques with respect to cloud detection and height assessment are also discussed. The standard MISR CTH retrieval is less sensitive to high thin cirrus than the Atmospheric Infrared Sounder (AIRS) and Cloud‐Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO), but MISR provides more accurate CTH retrievals in the middle and lower troposphere compared with other passive sensors, especially for clouds in the planetary boundary layer.
Determination of cloud condensation nuclei production from measured new particle formation events
Authors: Kuang C. , McMurry P. H. , McCormick A. V.
Published: May 2009

A semi‐analytical expression has been developed that accurately models the population dynamics of an aerosol growing from the detection limit (3 nm) to a characteristic CCN size (100 nm), quantifying the contributions of size and time‐dependent source and sink terms such as coagulation of smaller particles and scavenging by the pre‐existing aerosol. These model inputs were calculated from measured aerosol size distributions and growth rates acquired during intensive measurement campaigns in Boulder, CO, Atlanta, GA, and Tecamac, Mexico. Twenty CCN formation events from these campaigns were used to test the validity of this model. Measured growth rates ranged from 3–22 nm/h. The modeled and measured CCN production probabilities agreed well with each other, ranging from 1–20%. The pre‐existing CCN number concentration increased on average by a factor of 3.8 as a result of new particle formation.
Simultaneous generation of large‐scale density irregularities and geomagnetic pulsations via filamentation instability
Authors: Kuo Spencer P. , Cheng Wei‐Te , Cohen J. A. , Pradipta R. , Lee M. C. , Kuo Steven S. , Snyder Arnold
Published: May 2009

Results of experiment conducted at Gakona, Alaska, using intensity‐modulated HF heating waves of 3.2 MHz to generate geomagnetic pulsations and large‐scale field‐aligned density irregularities (FAI), are reported. The echo traces of o‐ and x‐mode sounding pulses from 3.53 to 4 MHz were recorded during heater on/off periods. The ionograms showed that only x‐mode echo traces were significantly affected by the HF heater. The returns from 3.53 to ∼3.8 MHz disappeared during heater on period and reappeared after heater was turned off. Ray tracings are performed to explore the effect of FAI on the backscattering of o‐ and x‐mode sounding pulses. The drastic difference between the FAI effects on o‐ and x‐mode backscattering trajectories provides a theoretical interpretation of the observation. Geomagnetic pulsations as large as 2.5 nT were also recorded by a Fluxgate Magnetometer. Thermal filamentation of the HF heater leads to the simultaneous generation of FAI and geomagnetic pulsations.
Voxel-Based Estimation of Kinetic Model Parameters of the l-[1-11C]Leucine PET Method for Determination of Regional Rates of Cerebral Protein Synthesis: Validation and Comparison with Region-of-Interest-Based Methods
Authors: Tomasi Giampaolo , Bertoldo Alessandra , Bishu Shrinivas , Unterman Aaron , Smith Carolyn Beebe , Schmidt Kathleen C
Published: May 2009

We adapted and validated a basis function method (BFM) to estimate at the voxel level parameters of the kinetic model of the l-[1-11C]leucine positron emission tomography (PET) method and regional rates of cerebral protein synthesis (rCPS). In simulation at noise levels typical of voxel data, BFM yielded low-bias estimates of rCPS; in measured data, BFM and nonlinear least-squares parameter estimates were in good agreement. We also examined whether there are advantages to using voxel-level estimates averaged over regions of interest (ROIs) in place of estimates obtained by directly fitting ROI time-activity curves (TACs). In both simulated and measured data, fits of ROI TACs were poor, likely because of tissue heterogeneity not taken into account in the kinetic model. In simulation, rCPS determined from fitting ROI TACs was substantially overestimated and BFM-estimated rCPS averaged over all voxels in an ROI was slightly underestimated. In measured data, rCPS determined by regional averaging of voxel estimates was lower than rCPS determined from ROI TACs, consistent with simulation. In both simulated and measured data, intersubject variability of BFM-estimated rCPS averaged over all voxels in a ROI was low. We conclude that voxelwise estimation is preferable to fitting ROI TACs using a homogeneous tissue model.
Rodent Neonatal Bilateral Carotid Artery Occlusion with Hypoxia Mimics Human Hypoxic-Ischemic Injury
Authors: Recker Rebecca , Adami Arash , Tone Beatriz , Tian Hui Rou , Lalas Serafin , Hartman Richard E , Obenaus André , Ashwal Stephen
Published: May 2009

We report a new clinically relevant model of neonatal hypoxic-ischemic injury in a 10-day-old rat pup. Bilateral carotid artery occlusion and 8% hypoxia (1 to 15 mins, BCAO-H) was induced with varying degrees of injury (mild, moderate, severe), which was quantified using magnetic resonance imaging including diffusion-weighted and T2-weighted imaging at 24 h and 21/28 days. We developed a magnetic resonance imaging-based rat pup severity score and compared 3D ischemic injury volumes/rat pup severity score with histology and behavioral testing. At 24 h, hypoxic-ischemic injury was observed in 17/27 animals; long-term survival was 81%. Magnetic resonance imaging lesion volumes did not correlate with hypoxia duration but correlated with rat pup severity score, which was used to classify animals into mild ( n = 21), moderate ( n = 6), and severe ( n = 10) groups with average brain lesion volumes of 0.9%, 33.2%, and 56.3%, respectively. Histology confirmed lesion location and histologic scoring correlated with the rat pup severity score. We also found excellent correlation between injury severity and multiple behavioral tasks. Bilateral carotid artery occlusion and hypoxia in the P10 rat pup is an excellent model of neonatal hypoxic-ischemic injury because it induces diffuse global injury similar to the term infant. This model can produce graded injury severity, similar to that seen in human neonates, but manipulation with hypoxia duration is unpredictable.
Dose-Dependent Effects of Androgens on Outcome after Focal Cerebral Ischemia in Adult Male Mice
Authors: Uchida Masayoshi , Palmateer Julie M , Herson Paco S , DeVries A Courtney , Cheng Jian , Hurn Patricia D
Published: May 2009

Males exhibit greater histologic and behavioral impairment after stroke than do age-matched females. However, the contribution of androgens to stroke outcome remains unclear. We compared outcomes from middle cerebral artery occlusion (MCAO) in castrated mice with those in testosterone- or dihydrotestosterone (DHT)-replaced castrated mice. Castrates treated with 1.5 mg testosterone or 0.5 mg DHT before MCAO showed smaller infarct volumes (hemisphere: 27 or 26%) at 24 h after 90 mins MCAO than did untreated castrates (37%), whereas 5 mg testosterone or 1.5 mg DHT exacerbated infarcts (53 or 51%). These outcomes were blocked by the androgen receptor antagonist, flutamide, suggesting that androgen receptors mediate these responses to ischemia. We further evaluated long-term outcomes with a milder 60-min MCAO in castrates treated with the protective 1.5 mg testosterone dose. Consistent with data obtained at 24 h reperfusion, the infarct volume was decreased at 9 days reperfusion. Neurobehavioral analysis showed that motor functional recovery was improved during the first 3 days of reperfusion, but not improved at 7 days. We conclude that testosterone exhibits dose-dependent and time-sensitive effects after ischemia and that testosterone is likely to be an important factor in sex-linked differences in cerebrovascular disease.
Red Blood Cells-Coupled tPA Prevents Impairment of Cerebral Vasodilatory Responses and Tissue Injury in Pediatric Cerebral Hypoxia/Ischemia through Inhibition of ERK MAPK Activation
Authors: Armstead William M , Ganguly Kumkum , Kiessling John W , Chen Xiao-Han , Smith Douglas H , Higazi Abd AR , Cines Douglas B , Bdeir Khalil , Zaitsev Sergei , Muzykantov Vladimir R
Published: May 2009

Babies experience hypoxia (H) and ischemia (I) from stroke. The only approved treatment for stroke is fibrinolytic therapy with tissue-type plasminogen activator (tPA). However, tPA potentiates H/I-induced impairment of responses to cerebrovasodilators such as hypercapnia and hypotension, and blockade of tPA-mediated vasoactivity prevents this deleterious effect. Coupling of tPA to red blood cells (RBCs) reduces its central nervous system (CNS) toxicity through spatially confining the drug to the vasculature. Mitogen-activated protein kinase (MAPK), a family of at least three kinases, is upregulated after H/I. In this study we determined whether RBC-tPA given before or after cerebral H/I would preserve responses to cerebrovasodilators and prevent neuronal injury mediated through the extracellular signal-related kinase (ERK) MAPK pathway. Animals given RBC-tPA maintained responses to cerebrovasodilators at levels equivalent to pre-H/I values. cerebrospinal fluid and brain parenchymal ERK MAPK was elevated by H/I and this upregulation was potentiated by tPA, but blunted by RBC-tPA. U0126, an ERK MAPK antagonist, also maintained cerebrovasodilation post H/I. Neuronal degeneration in CA1 hippocampus after H/I was not improved by tPA, but was ameliorated by RBC-tPA and U0126. These data suggest that coupling of tPA to RBCs offers a novel approach toward increasing the benefit/risk ratio of thrombolytic therapy for CNS disorders associated with H/I.
Committed Neural Progenitor Cells Derived from Genetically Modified Bone Marrow Stromal Cells Ameliorate Deficits in a Rat Model of Stroke
Authors: Hayase Makoto , Kitada Masaaki , Wakao Shohei , Itokazu Yutaka , Nozaki Kazuhiko , Hashimoto Nobuo , Takagi Yasushi , Dezawa Mari
Published: May 2009

Bone marrow stromal cells (MSCs) are an excellent source of cells for treating a variety of central nervous system diseases. In this study, we report the efficient induction of committed neural progenitor cells from rat and human MSCs (NS-MSCs) by introduction of cells with the intracellular domain of Notch-1 followed by growth in the free-floating culture system. NS-MSCs successfully formed spheres, in which cells highly expressed the neural precursor cell markers. The commitment of spheres to neural lineage cells was confirmed by their successful differentiation into neuronal cells when exposed to a differentiation medium. To determine the therapeutic potential of NS-MSCs, cells were transplanted into the cortex and striatum in a rat model of focal cerebral ischemia. The survival, distribution, and integration of NS-MSCs in the host brain were very high, and at day 100, grafted NS-MSCs were positive for dopaminergic, glutamatergic, and γ-amino butyric acid (GABA)ergic neuronal markers. They extended long neurites for nearly 6.3 mm and many of these expressed synaptophysin. Significant behavioral recovery was also observed in limb-placing and water-maze tests. These suggest a high potential for this MSC approach in the replenishment of neural cells for stroke and for a wide range of neurodegenerative conditions that require various types of neural cells.
Cancer Biology Data Curation at the Mouse Tumor Biology Database (MTB)
Authors: Krupke Debra , Begley Dale , Neuhauser Steven , Richardson Joel , Sundberg John , Bult Carol , Eppig Janan
Published: May 2009

Many advances in the field of cancer biology have been made using mouse models of human cancer. The Mouse Tumor Biology (MTB, "http://tumor.informatics.jax.org":http://tumor.informatics.jax.org) database provides web-based access to data on spontaneous and induced tumors from genetically defined mice (inbred, hybrid, mutant, and genetically engineered strains of mice). These data include standardized tumor names and classifications, pathology reports and images, mouse genetics, genomic and cytogenetic changes occurring in the tumor, strain names, tumor frequency and latency, and literature citations.Although primary source for the data represented in MTB is peer-reviewed scientific literature an increasing amount of data is derived from disparate sources. MTB includes annotated histopathology images and cytogenetic assay images for mouse tumors where these data are available from The Jackson Laboratory’s mouse colonies and from outside contributors. MTB encourages direct submission of mouse tumor data and images from the cancer research community and provides investigators with a web-accessible tool for image submission and annotation. Integrated searches of the data in MTB are facilitated by the use of several controlled vocabularies and by adherence to standard nomenclature. MTB also provides links to other related online resources such as the Mouse Genome Database, Mouse Phenome Database, the Biology of the Mammary Gland Web Site, Festing's Listing of Inbred Strains of Mice, the JAX® Mice Web Site, and the Mouse Models of Human Cancers Consortium's Mouse Repository. MTB provides access to data on mouse models of cancer via the internet and has been designed to facilitate the selection of experimental models for cancer research, the evaluation of mouse genetic models of human cancer, the review of patterns of mutations in specific cancers, and the identification of genes that are commonly mutated across a spectrum of cancers.MTB is supported by NCI grant CA089713.
Biocuration Workflow Catalogue
Authors: Burns Gully , Krallinger Martin , Cohen Kevin , Wu Cathy , Hirschman Lynette
Published: May 2009

As the first phase of a knowledge engineering study of biocuration workflows, we performed a preliminary task-modeling exercise on seven separate bioinformatics systems. This involved constructing UML activity diagrams from detailed interviews with curators in order to understand the organization of the process the biocurators used to populate their system. The objective of this work was to identify common patterns within the workflows where we might apply text mining methods to accelerate curation. We compiled a number of workflows in a common format but were largely unable to consolidate these structures into a formal structure that facilitated comparison across workflows. We presented this work as a slideshow and publish this account of the catalog as supplementary information.
The ESCRT‐III protein CeVPS‐32 is enriched in domains distinct from CeVPS‐27 and CeVPS‐23 at the endosomal membrane of epithelial cells
Authors: Michelet Xavier , Alberti Adriana , Benkemoun Laura , Roudier Nathalie , Lefebvre Christophe , Legouis Renaud
Published: May 2009

Background information. Within the endocytic pathway, the ESCRT (endosomal sorting complex required for transport) machinery is essential for the biogenesis of MVBs (multivesicular bodies). In yeast, ESCRTs are recruited at the endosomal membrane and are involved in cargo sorting into intralumenal vesicles of the MVBs.

Results. In the present study, we characterize the ESCRT‐III protein CeVPS‐32 (Caenorhabditis elegans vacuolar protein sorting 32) and its interactions with CeVPS‐27, CeVPS‐23 and CeVPS‐4. In contrast with other CevpsE (class E vps) genes, depletion of Cevps‐32 is embryonic lethal with severe defects in the remodelling of epithelial cell shape during organogenesis. Furthermore, Cevps‐32 animals display an accumulation of enlarged early endosomes in epithelial cells and an accumulation of autophagosomes. The CeVPS‐32 protein is enriched in epithelial tissues and in residual bodies during spermatid maturation. We show that CeVPS‐32 and CeVPS‐27/Hrs (hepatocyte‐growth‐factor‐regulated tyrosine kinase substrate) are enriched in distinct subdomains at the endosomal membrane. CeVPS‐27‐positive subdomains are also enriched for the ESCRT‐I protein CeVPS‐23/TSG101 (tumour susceptibility gene 101). The formation of CeVPS‐27 subdomains is not affected by the depletion of CeVPS‐23, CeVPS‐32 or the ATPase CeVPS‐4.

Conclusion. Our results suggest that the formation of membrane subdomains is essential for the maturation of endosomes.
PKCϵ has an alcohol-binding site in its second cysteine-rich regulatory domain
Authors: Das Joydip , Pany Satyabrata , Rahman Ghazi M. , Slater Simon J.
Published: May 2009

Alcohols regulate the expression and function of PKC (protein kinase C), and it has been proposed that an alcohol-binding site is present in PKCα in its C1 domain, which consists of two cysteine-rich subdomains, C1A and C1B. A PKCϵ-knockout mouse showed a significant decrease in alcohol consumption compared with the wild-type. The aim of the present study was to investigate whether an alcohol-binding site could be present in PKCϵ. Here we show that ethanol inhibited PKCϵ activity in a concentration-dependent manner with an EC50 (equilibrium ligand concentration at half-maximum effect) of 43 mM. Ethanol, butanol and octanol increased the binding affinity of a fluorescent phorbol ester SAPD (sapintoxin-D) to PKCϵC1B in a concentration-dependent manner with EC50 values of 78 mM, 8 mM and 340 μM respectively, suggesting the presence of an allosteric alcohol-binding site in this subdomain. To identify this site, PKCϵC1B was photolabelled with 3-azibutanol and 3-azioctanol and analysed by MS. Whereas azibutanol preferentially labelled His236, Tyr238 was the preferred site for azioctanol. Inspection of the model structure of PKCϵC1B reveals that these residues are 3.46 Å (1 Å=0.1 nm) apart from each other and form a groove where His236 is surface-exposed and Tyr238 is buried inside. When these residues were replaced by alanine, it significantly decreased alcohol binding in terms of both photolabelling and alcohol-induced SAPD binding in the mutant H236A/Y238A. Whereas Tyr238 was labelled in mutant H236A, His236 was labelled in mutant Y238A. The present results provide direct evidence for the presence of an allosteric alcohol-binding site on protein kinase Cϵ and underscore the role of His236 and Tyr238 residues in alcohol binding.
Quinalizarin as a potent, selective and cell-permeable inhibitor of protein kinase CK2
Authors: Cozza Giorgio , Mazzorana Marco , Papinutto Elena , Bain Jenny , Elliott Matthew , di Maira Giovanni , Gianoncelli Alessandra , Pagano Mario A. , Sarno Stefania , Ruzzene Maria , Battistutta Roberto , Meggio Flavio , Moro Stefano , Zagotto Giuseppe , Pinna Lorenzo A.
Published: May 2009

Emodin (1,3,8-trihydroxy-6-methyl-anthraquinone) is a moderately potent and poorly selective inhibitor of protein kinase CK2, one of the most pleiotropic serine/threonine protein kinases, implicated in neoplasia and in other global diseases. By virtual screening of the MMS (Molecular Modeling Section) database, we have now identified quinalizarin (1,2,5,8-tetrahydroxyanthraquinone) as an inhibitor of CK2 that is more potent and selective than emodin. CK2 inhibition by quinalizarin is competitive with respect to ATP, with a Ki value of approx. 50 nM. Tested at 1 μM concentration on a panel of 75 protein kinases, quinalizarin drastically inhibits only CK2, with a promiscuity score (11.1), which is the lowest ever reported so far for a CK2 inhibitor. Especially remarkable is the ability of quinalizarin to discriminate between CK2 and a number of kinases, notably DYRK1a (dual-specificity tyrosine-phosphorylated and -regulated kinase), PIM (provirus integration site for Moloney murine leukaemia virus) 1, 2 and 3, HIPK2 (homeodomain-interacting protein kinase-2), MNK1 [MAPK (mitogen-activated protein kinase)-interacting kinase 1], ERK8 (extracellular-signal-regulated kinase 8) and PKD1 (protein kinase D 1), which conversely tend to be inhibited as drastically as CK2 by commercially available CK2 inhibitors. The determination of the crystal structure of a complex between quinalizarin and CK2α subunit highlights the relevance of polar interactions in stabilizing the binding, an unusual characteristic for a CK2 inhibitor, and disclose other structural features which may account for the narrow selectivity of this compound. Tested on Jurkat cells, quinalizarin proved able to inhibit endogenous CK2 and to induce apoptosis more efficiently than the commonly used CK2 inhibitors TBB (4,5,6,7-tetrabromo-1H-benzotriazole) and DMAT (2-dimethylamino-4,5,6,7-tetrabromo-1H-benzimidazole).
Variably modulated gating of the 26S proteasome by ATP and polyubiquitin
Authors: Li Xiaohua , Demartino George N.
Published: May 2009

The 26S proteasome is a 2500 kDa protease complex that degrades polyubiquitylated proteins by a mechanism that requires ATP hydrolysis. It also degrades short non-ubiquitylated peptides and certain unstructured proteins by an energy-independent mechanism that requires bound ATP to maintain its component subcomplexes, the 20S proteasome and PA700, in a functionally assembled state. Proteolysis of both types of substrate requires PA700-induced opening of reversible gates at substrate-access pores of the 20S proteasome. In the present study we demonstrate that the rate of peptide substrate hydrolysis, a functional monitor of gate opening, is regulated variably by multiple effectors. ATPγS (adenosine 5′-[γ-thio]triphosphate) and other non-hydrolysable ATP analogues increased peptide substrate hydrolysis by intact 26S proteasomes. Thus nucleotides that maintained 26S proteasome structure, but did not support ATP hydrolysis or the degradation of polyubiquitylated proteins, promoted enhanced rates of peptide hydrolysis. Polyubiquitin and a peptoid that binds selectively to a single ATPase subunit of PA700 also increased rates of peptide hydrolysis but had disparate effects on rates of ATP hydrolysis. The effect of polyubiquitin was specific for ubiquitin–ubiquitin linkages that supported proteolysis of protein substrates. These results indicate that gating of the 26S proteasome is not a simple two-state process but can be variably modulated. Our results suggest that modulated gating of the proteasome may be an important element of the mechanism of proteolysis of polyubiquitylated proteins.
ARHI (DIRAS3), an imprinted tumour suppressor gene, binds to importins and blocks nuclear import of cargo proteins
Authors: Huang Shaoyi , Soon Chang In , Lin Wenbo , Ye Wenduo , Luo Robert Z. , Lu Zhen , Lu Yiling , Zhang Ke , Liao Warren S.-L. , Tao Tao , Bast Robert C. , Chen Xiaomin , Yu Yinhua
Published: May 2009

ARHI (aplasia Ras homologue member I; also known as DIRAS3) is an imprinted tumour suppressor gene, the expression of which is lost in the majority of breast and ovarian cancers. Unlike its homologues Ras and Rap, ARHI functions as a tumour suppressor. Our previous study showed that ARHI can interact with the transcriptional activator STAT3 (signal transducer and activator of transcription 3) and inhibit its nuclear translocation in human breast- and ovarian-cancer cells. To identify proteins that interact with ARHI in nuclear translocation, in the present study, we performed proteomic analysis and identified several importins that can associate with ARHI. To further explore this novel finding, we purified 10 GST (glutathione transferase)–importin fusion proteins (importins 7, 8, 13, β1, α1, α3, α5, α6, α7 and mutant α1). Using a GST-pulldown assay, we found that ARHI can bind strongly to most importins; however, its binding is markedly reduced with an importin α1 mutant that contains an altered NLS (nuclear-localization signal) domain. In addition, an ARHI N-terminal deletion mutant exhibits greatly reduced binding to all importins compared with wild-type ARHI. In nuclear-import assays, the addition of ARHI blocked nuclear localization of phosphorylated STAT3. ARHI also inhibits the interaction of Ran–importin complexes with GFP (green fluorescent protein) fusion proteins that contain an NLS domain and a β-like import receptor-binding domain, thereby blocking their nuclear localization. By conducting GST-pulldown assays, we found that ARHI could compete for Ran-importin binding. Thus ARHI-induced disruption of importin-binding to cargo proteins, including STAT3, could serve as an important regulatory mechanism that contributes to the tumour-suppressor function of ARHI.
Imprinting analysis in the Acrodysplasia region of mouse chromosome 12
Authors: McMurray Erin N. , Rogers Eric D. , Schmidt Jennifer V.
Published: May 2009

The insertional mouse mutation Adp (Acrodysplasia) confers a parent-of-origin developmental phenotype, with animals inheriting the mutation from their father showing skeletal abnormalities, whereas those inheriting the mutation from their mother are normal. This parental-specific phenotype, along with mapping of the insertion to a region of chromosome 12 proposed to contain imprinted genes, suggested that disruption of genomic imprinting might underlie the Adp phenotype. Genomic imprinting is the process by which autosomal genes are epigenetically silenced on one of the two parental alleles; imprinting mutation phenotypes manifest after inheritance from one parent but not the other. Imprinted genes typically occur in dense clusters that contain few non-imprinted genes and therefore representative genes from the Adp critical region could be assayed to identify any imprinted domains. None of the genes analysed were found to be imprinted, however, suggesting that other explanations for the Adp phenotype must be considered.
Advances in Nucleic Acid Detection and Quantification
Authors: Kavanagh Ian C. , Baker Simon C.
Published: May 2009

The last decade has seen many changes in molecular biology at the bench, as we have moved away from a primary goal of cataloguing genes and mRNA towards techniques that detect and quantify nucleic acid molecules even within single cells. With the invention of the polymerase chain reaction (PCR), a nucleic acid sequence could now be amplified to generate a large number of identical copies, and this launched a new era in genetic research. PCR has developed in parallel to fluorescent hybridization probing to provide low-, medium- and high-throughput detection methods. However, PCR and hybridization detection have significant drawbacks as long-term solutions for routine research and diagnostics assays. Therefore many novel methods are being developed independently, but as yet no one technique has emerged as a clear replacement for PCR, microarrays or even sequencing. In order to examine the technological horizon in this area, around 90 delegates assembled at Hinxton Hall, Cambridge, U.K. on 28 and 29 October 2008 for a Biochemical Society/Wellcome Trust Focused Meeting sponsored by Thermo Fisher Scientific and the British Library. The title of the meeting was ‘Advances in Nucleic Acid Detection and Quantification’, and the primary aim was to bring together scientists from different disciplines who nevertheless are trying to develop reliable methods for the quantification or detection of RNA and DNA molecules. This meant that physical and organic chemists, microbial ecologists and clinicians appeared alongside molecular biologists. An introductory session on general nucleic acid detection technologies was initiated with a fascinating insight into single-molecule, singlecell hybridization from Professor Sir Edwin Southern. This served as an ideal base for sessions on single-cell molecular biology and an examination of current applications of emerging technology. This issue of Biochemical Society Transactions contains some of the papers prepared by speakers at the meeting, and highlights not only how PCR and microarrays are already being replaced, but also which methods are likely to replace them.
Modeling and experiments on diffusion and activation of phosphorus in germanium
Authors: Tsouroutas P. , Tsoukalas D. , Zergioti I. , Cherkashin N. , Claverie A.
Published: May 2009

We report on phosphorus diffusion and activation related phenomena in germanium. We have used both conventional thermal processing and laser annealing by pulsed nanosecond Nd:YAG laser. Chemical profiles were obtained by secondary-ion-mass spectroscopy, sheet resistance was estimated by the van der Pauw method, and structural defects were monitored by transmission electron microscopy. Our study covers the temperature range from 440 to 750 °C, and we were able to efficiently simulate the dopant profiles within that temperature range, taking into account a quadratic dependence of the P diffusion coefficient on the free electron concentration. To achieve that we have taken into account dopant activation dependence on temperature as well as dopant pile-up near the surface and dopant loss owing to outdiffusion during the annealing. A combined laser thermal treatment above the melting threshold prior to conventional annealing allowed the elimination of the implantation damage, so we could perceive the influence of defects on both transient dopant diffusion and outdiffusion.
The effect of morphology upon mobility: Implications for bulk heterojunction solar cells with nonuniform blend morphology
Authors: Groves C. , Koster L. J. A. , Greenham N. C.
Published: May 2009

We use a Monte Carlo model to predict the effect of composition, domain size, and energetic disorder upon the mobility of carriers in an organic donor-acceptor blend. These simulations show that, for the changes in local morphology expected within the thickness of a typical bulk heterojunction photovoltaic device, changes in mobility of more than an order of magnitude are expected. The impact of nonuniform mobility upon space-charge-limited diode and photovoltaic (PV) device performance is examined using a drift-diffusion model. The current passing through a space-charge-limited diode is shown to depend upon the position of the layers with differing mobility. Accurate modeling of the current in such devices can only be achieved using a drift-diffusion model incorporating nonuniform mobility. Inserting a 20 nm thick layer in which the mobility is less by one order of magnitude than in the rest of the 70 nm thick PV device reduced the device efficiency by more than 20%. Therefore it seems vital to exert a high degree of control over the morphology throughout the entire blend PV device, otherwise potential PV performance may be lost.
Four switching categories of ferroelectrics
Authors: Lou X. J.
Published: May 2009

We classify the switching kinetics of ferroelectrics including both epitaxial/polycrystalline thin films and single-crystalline/ceramic bulks at various applied fields into four categories, depending on whether the depolarization field and/or the polarization reversal induced by the switching promotion effect between adjacent parts can be neglected. We show that our statistical model developed very recently [X. J. Lou, J. Phys.: Condens. Matter 21, 012207 (2009)] in its generalized form applies to all these four categories. Finally, we make the comparison between our model and the conventional Kolmogorov–Avrami–Ishibashi model and discuss the behavior of the switching currents for different n.
The ground state rotational spectrum of the fluorosulfate radical
Authors: Kolesniková Lucie , Varga Juraj , Stříteská Lucie Nová , Beckers Helmut , Willner Helge , Aubke Friedhelm , Urban Štěpán
Published: May 2009

The rotational spectra of the fluorosulfate (FSO3⋅) molecular radical in its vibronic ground state were measured in the millimeter-wave region and analyzed in detail using the matrix elements of the rotational, fine, and hyperfine Hamiltonian terms. The analysis of the assigned transition frequencies made it possible to derive very precise values of the rotational, centrifugal distortion and fine structure constants and to confirm the C3v molecular symmetry of the vibronic ground state unambiguously. In addition, an effective parameter of the “A1-A2 splitting” was determined. The rotational transitions of the FSO3⋅ free radical were observed, identified, and analyzed for the first time.
Analytic response theory for the density matrix renormalization group
Authors: Dorando Jonathan J. , Hachmann Johannes , Chan Garnet Kin-Lic
Published: May 2009

We propose an analytic response theory for the density matrix renormalization group, whereby response properties correspond to analytic derivatives of density matrix renormalization group observables with respect to the applied perturbations. Both static and frequency-dependent response theories are formulated and implemented. We evaluate our pilot implementation by calculating static and frequency-dependent polarizabilities of short oligodiacetylenes. The analytic response theory is competitive with dynamical density matrix renormalization group methods and yields significantly improved accuracies when using a small number of density matrix renormalization group states. Strengths and weaknesses of the analytic approach are discussed.
Dynamic modeling of a midinfrared quantum cascade laser
Authors: Hamadou A. , Lamari S. , Thobel J.-L.
Published: May 2009

Based on a three-level rate equations model, we analyze through numerical simulations the population and photon number dynamics present within the cavity of a midinfrared quantum cascade laser. We find in particular that the injection current influences significantly the electron number dynamics trajectory. In addition, the equations that allow for the determination of the turn-on delay (tth) and buildup (Δt) times are derived within the premises of our model in the most general case. The effects of the spontaneous emission factor β on Δt are also explored.
A simulation study of fast ignition with ultrahigh intensity lasers
Authors: Tonge J. , May J. , Mori W. B. , Fiuza F. , Martins S. F. , Fonseca R. A. , Silva L. O. , Ren C.
Published: May 2009

The coupling efficiency between the ignition laser and the target core for the fast ignition concept is studied using two-dimensional particle-in-cell simulations. The details of the energy transport within the weakly collisional overdense plasma of a fast ignition target are examined by performing a series of particle-in-cell simulations, where the intensity incident on a 100 times critical plasma with 50 μm radius is varied between each simulation. The simulations show that the peak energy flux of the ignition electrons is significantly lowered as the electrons traverse the collisionless plasma from the critical density through a weakly collisional overdense plasma region. This allows higher intensity lasers to be used thereby improving the coupling efficiency. In addition, we find that a higher percentage of the ignition laser energy is delivered to the core of the simulation target at higher intensity. The coupling efficiency increases in time during the simulations which are run for 2.5 ps. For a laser intensity of 8×1020 W/cm2 the simulations indicate that more than 15% of the incident laser energy is eventually absorbed in a dense plasma core.
On the electron whistler dispersion law in a cold plasma with light ions and heavy charged particulates
Authors: Lundin B. V. , Krafft C.
Published: May 2009

The dispersion equation of electron whistler waves in a cold plasma with two light ions of comparable gyrofrequencies and heavy charged particulates is derived. It is valid in a very wide frequency range above the highest ion cutoff frequency when the wave frequency is essentially less than the electron plasma frequency. The derived electron whistler dispersion law is expressed through the relative contents of the two light ions and the electrons, as well as the characteristic frequencies of the magnetized plasma, as the lower hybrid resonance frequency, the two highest ion cutoff frequencies, the gyrofrequencies of the light ions, and the electron gyro- and plasma frequencies. The approximation of vanishingly small gyrofrequencies of the heavy ions permits to determine with a relevant accuracy the electron whistler dispersion law using the features of electron whistler spectrograms only. Estimates of the relative charge density of the light ions are obtained and the dispersion laws of the adjacent branches, i.e., the electron whistler waves and the so-called ion cyclotron whistlers are calculated. For the electron whistler waves, the presence of negative ions can be the origin of a manyfold increase in the lower cutoff frequency; a merging effect of the cutoff frequencies of the adjacent branches can also appear.
Investigations of acceptor related photoluminescence from electrodeposited Ag-doped ZnO
Authors: Thomas M. A. , Cui J. B.
Published: May 2009

The effects of Ag doping on the photoluminescence (PL) of low temperature grown ZnO have been investigated. Ag-doped ZnO exhibited distinguished PL characteristics from the undoped material. An intense emission at 3.323 eV from a free electron to bound acceptor transition was observed in the Ag-doped ZnO, while a donor bound exciton transition dominated the band edge emission for undoped ZnO. The acceptor binding energy of 117 meV calculated from the temperature dependent PL is consistent with the reported values. This spectroscopic investigation indicates that Ag can be introduced into the host material by a cost-efficient electrochemical process and is a potential p-type dopant for ZnO.
High-temperature thermoelectric properties of Ca0.9−xSrxYb0.1MnO3−δ (≤x≤0.2)
Authors: Kosuga Atsuko , Isse Yuri , Wang Yifeng , Koumoto Kunihito , Funahashi Ryoji
Published: May 2009

Polycrystalline samples of Ca0.9−xSrxYb0.1MnO3−δ (x=0, 0.025. 0.05, 0.1, and 0.2) were prepared by a conventional solid-state reaction and their thermoelectric properties were evaluated at 303–973 K. Each of the samples consisted of a single phase with an orthorhombic structure. All the samples showed a metallic conductivity and their electrical resistivity was markedly affected by the distortion of the MnO6 octahedron. The Seebeck coefficient of all the samples was negative, indicating that the predominant carriers were electrons over the entire temperature range examined. The highest power factor achieved (0.22 mW m−1 K−2 at 773 K) was shown by the sample with x=0.1. The thermal conductivity was affected by both the crystal distortion and the difference in mass between the Ca2+ and Sr2+ ions. The highest dimensionless figure of merit obtained was 0.09 at 973 K for the sample with x=0.1; this is a result of its low electrical resistivity and its moderate Seebeck coefficient and thermal conductivity.
Maximum energy transfer in near-field thermal radiation at nanometer distances
Authors: Basu S. , Zhang Z. M.
Published: May 2009

Radiative energy transfer at nanoscale distances can exceed that of blackbody radiation by several orders of magnitude due to photon tunneling and the excitation of surface polaritons. While significant progress has been made recently in understanding near-field thermal radiation, an outstanding question remains as whether there exists an upper limit of near-field radiation for arbitrarily selected material properties at finite separation distances. We investigate the maximum achievable radiative heat flux between two parallel plates separated by a vacuum gap from 0.1 to 100 nm. By assuming a frequency-independent dielectric function and introducing a cutoff parallel wavevector component, we find that the ideal dielectric function for the two media that will maximize the near-field radiative transfer is −1+iδ, where δ is the imaginary part. For vacuum gaps greater than 1 nm, the near-field heat transfer peaks when δ⪡1, while at subnanometer gaps, the peak in the energy transfer shifts toward larger values of δ. The determination of the maximum radiative flux at nanometer distances will benefit emerging applications of near-field radiation for energy harvesting and nanothermal manufacturing.
Curvature estimate for multilayer rolled-up nanostructures with cubic crystal anisotropy under initial strains
Authors: Nishidate Y. , Nikishkov G. P.
Published: May 2009

The generalized plane strain solution for anisotropic multilayer nanostructures with cubic crystal symmetry under the influence of initial strains has been derived. This solution can be used to estimate equilibrium curvature radius and strains/stresses of rolled-up anisotropic multilayer nanostructures, whose deformations are induced by crystal lattice mismatch. The solution has been applied for calculation of curvature radii and strain components of a bilayer In0.2Ga0.8As/GaAs rolled-up nanostructure. The results are in agreement with those obtained by a finite element analysis.
Impact of the chemical concentration on the solid-phase epitaxial regrowth of phosphorus implanted preamorphized germanium
Authors: Simoen E. , Brugère A. , Satta A. , Firrincieli A. , Van Daele B. , Brijs B. , Richard O. , Geypen J. , Meuris M. , Vandervorst W.
Published: May 2009

The impact of the phosphorus concentration [P] on the solid-phase epitaxial regrowth rate of preamorphized p-type germanium has been studied by a combination of Rutherford backscattering, secondary ion mass spectrometry, and transmission electron microscopy. It will be shown that for P concentrations in the 1018–5×1019 cm−3 range, the regrowth rate is significantly enhanced compared with undoped germanium, while the opposite holds for [P] above about 4–5×1020 cm−3. This regrowth retardation is shown associated with segregation across the crystalline/amorphous boundary and snow plow of P in excess of the metastable solid solubility in the recrystallized material.
Direct evidence of phase separation in Ge2Sb2Te5 in phase change memory devices
Authors: Kim Cheolkyu , Kang Dongmin , Lee Tae-Yon , Kim Kijoon H. P. , Kang Youn-Seon , Lee Junho , Nam Sung-Wook , Kim Ki-Bum , Khang Yoonho
Published: May 2009

Phase change materials in phase change random access memory (PRAM) undergo very high electrical stress as well as thermal stress during operation. These can cause intrinsic problems in stability of the PRAM devices. We investigate the stability of Ge2Sb2Te5, the most common phase change material for PRAM, under electrical stress. After multiple programming cycles, cross-sectional transmission electron microscopy and energy dispersive analysis show that electromigration as well as incongruent melting causes phase separation by mass movement by which the peak position of Sb and Ge lies shifted toward the cathode and that of Te toward the anode.
High resolution laser induced fluorescence Doppler velocimetry utilizing saturated absorption spectroscopy
Authors: Aramaki Mitsutoshi , Ogiwara Kohei , Etoh Shuzo , Yoshimura Shinji , Tanaka Masayoshi Y.
Published: May 2009

A high resolution laser induced fluorescence (LIF) system has been developed to measure the flow velocity field of neutral particles in an electron-cyclotron-resonance argon plasma. The flow velocity has been determined by the Doppler shift of the LIF spectrum, which is proportional to the velocity distribution function. Very high accuracy in velocity determination has been achieved by installing a saturated absorption spectroscopy unit into the LIF system, where the absolute value and scale of laser wavelength are determined by using the Lamb dip and the fringes of a Fabry–Pérot interferometer. The minimum detectable flow velocity of a newly developed LIF system is ±2 m/s, and this performance remains unchanged in a long-time experiment. From the radial measurements of LIF spectra of argon metastable atoms, it is found that there exists an inward flow of neutral particles associated with neutral depletion.
Electron-pair radial sum and difference density functions
Authors: Koga Toshikatsu , Sekiya Masahiro
Published: May 2009

For deeper understanding of electron-electron radial holes, we introduce and discuss electron-pair radial sum S(s) and difference T(t) density functions, which respectively represent the probability densities for the radial sum s=r1+r2 and difference t=r1−r2 variables of two electrons. Fundamental properties of the densities S(s) and T(t) are clarified. The appearance of radial holes given by T(0)=0 is shown to have a nontrivial effect on the sum density S(s) as well. Numerical illustrations are given for the 1s2s S1 and S3 states of the helium atom and for the ground state of the lithium atom.
Plasma expansion and fast gap closure in a high power electron beam diode
Authors: Roy Amitava , Menon R. , Mitra S. , Kumar Senthil , Sharma Vishnu , Nagesh K. V. , Mittal K. C. , Chakravarthy D. P.
Published: May 2009

High power electron beam generation studies were carried out in a planar diode configuration to investigate the effect of the accelerating gap, diode voltage, and anode-cathode materials on the electrode plasma expansion. The diode voltage has been varied from 145–428 kV, whereas the current density has been varied from 208–2215 A/cm2 with 100 ns pulse duration. It was found that the diode voltage and current follow the bipolar space-charge limited flow model. The anode and cathode plasma expansion velocities were calculated using the perveance data. The plasma expands at 11 cm/μs for 34 mm anode-cathode gap and the plasma velocity decreases for smaller gaps. It was found that the plasma expansion velocity increases significantly due to the cathode edge contribution and the edge contribution is particularly important during the beginning and the end of the accelerating pulse when the diode voltage and the corresponding electric field are comparatively low. It was also observed that the diode current increased by a factor of 3 when anode material was released into the accelerating gap due to the electron beam bombardment.
A versatile fiber-optic coupled system for sensitive optical spectroscopy in strong ambient light
Authors: Sinha Sudarson Sekhar , Verma Pramod Kumar , Makhal Abhinandan , Pal Samir Kumar
Published: May 2009

In this work we describe design and use of a fiber-optic based optical system for the spectroscopic studies on the samples under the presence of strong ambient light. The system is tested to monitor absorption, emission, and picosecond-resolved fluorescence transients simultaneously with a time interval of 500 ms for several hours on a biologically important sample (vitamin B2) under strong UV light. An efficient stray-light rejection ratio of the setup is achieved by the confocal geometry of the excitation and detection channels. It is demonstrated using this setup that even low optical signal from a liquid sample under strong UV-exposure for the picosecond-resolved fluorescence transient measurement can reliably be detected by ultrasensitive microchannel plate photomultiplier tube solid state detector. The kinetics of photodeterioration of vitamin B2 measured using our setup is consistent with that reported in the literature. Our present studies also justify the usage of tungsten light than the fluorescent light for the healthy preservation of food with vitamin B2.
Warm electromagnetic lower hybrid wave dispersion relation
Authors: Verdon A. L. , Cairns Iver H. , Melrose D. B. , Robinson P. A.
Published: May 2009

Lower hybrid (LH) waves can interact resonantly with both electrons and ions transferring energy between the species. For this reason the properties of LH waves are of interest. Most treatments of LH waves include either electromagnetic (EM) or warm plasma effects but not both. Here a new analytic dispersion relation for LH waves, including both EM and warm plasma effects, is derived and shown to be more consistent than the previous analytic dispersion relations with numerical results. These comparisons show a very good agreement of the real part of the frequency and reasonable agreement of the imaginary part for a wide range of parameters. It is found that ion magnetization effects, which have been neglected in all previous analytic treatments of LH waves, are surprisingly important. When ion magnetization effects become important the continuous LH mode breaks up into a series of segments of ion Bernstein modes.