bluuebunny/crossref_metadata_2025 huggingface dataset:
Simultaneous measurement of benzo[a]pyrene‐induced Pig‐a and lacZ mutations, micronuclei and dna adducts in mutaTMmouse
Authors: Lemieux Christine L. , Douglas George R. , Gingerich John , Phonethepswath Souk , Torous Dorothea K , Dertinger Stephen D. , Phillips David H. , Arlt Volker M. , White Paul A.
Published: October 2011

In this study we compared the response of the Pig‐a gene mutation assay to that of the lacZ transgenic rodent mutation assay, and demonstrated that multiple endpoints can be measured in a 28‐day repeat dose study. Muta™Mouse were dosed daily for 28 days with benzo[a]pyrene (BaP; 0, 25, 50 and 75 mg/kg body weight/day) by oral gavage. Micronucleus (MN) frequency was determined in reticulocytes (RETs) 48 hr following the last dose. 72 h following the last dose, mice were euthanized, and tissues (glandular stomach, small intestine, bone marrow and liver) were collected for lacZ mutation and DNA adduct analysis, and blood was evaluated for Pig‐a mutants. BaP‐derived DNA adducts were detected in all tissues examined and significant dose‐dependent increases in mutant Pig‐a phenotypes (i.e., RETCD24‐ and RBC CD24‐) and lacZ mutants were observed. We estimate that mutagenic efficiency (i.e., rate of conversion of adducts into mutations) was much lower for Pig‐a compared to lacZ, and speculate that this difference is likely explained by differences in repair capacity between the gene targets, and differences in the cell populations sampled for Pig‐a versus lacZ. The BaP doubling doses for both gene targets, however, were comparable, suggesting that similar mechanisms are involved in the accumulation of gene mutations. Significant dose‐related increases in % MN were also observed; however, the doubling dose was considerably higher for this endpoint. The similarity in dose response kinetics of Pig‐a and lacZ provides further evidence for the mutational origin of glycosylphosphatidylinositol (GPI)‐anchor deficiencies detected in the Pig‐a assay. Environ. Mol. Mutagen. 2011. © 2011 Wiley‐Liss, Inc.
Small soil storage capacity limits benefit of winter snowpack to upland vegetation
Authors: Smith T. J. , McNamara J. P. , Flores A. N. , Gribb M. M. , Aishlin P. S. , Benner S. G.
Published: October 2011

In the western United States, the mountain snowpack is an important natural reservoir that extends spring and summer water delivery to downstream users and ecosystems. The importance of winter snow accumulation to upland ecosystems is not as clearly defined. This study investigates the relative contribution of winter precipitation to upland spring and summer soil moisture storage and availability in a semi‐arid mountainous watershed. At this site, coarse soil textures and shallow soil depths limit soil storage capacity to 6–16 cm. Winter precipitation exceeds soil storage capacity by 2.5 times. Accordingly, soil moisture profiles at most locations in the watershed reach field capacity in early winter. With soil storage near capacity, water released by snowmelt primarily contributes to deep drainage and makes a limited contribution to the soil moisture reservoir. Water that is retained by the soil after the snowpack melts is lost to evapotranspiration in as little as 10 days. In contrast, spring precipitation extends moist soil conditions by up to 90 days into the warm season, when ecological water demand is highest. These field observations suggest that changes in spring precipitation, not winter snowpack, may have the greater impact on upland ecosystems in this environment. Furthermore, because winter precipitation is in excess compared to the soil storage capacity, soil moisture availability may be fairly insensitive to climate change‐induced transitions from snow to rain. Copyright © 2011 John Wiley & Sons, Ltd.
Did China diversify its foreign reserves?
Authors: Sheng Liugang
Published: October 2011

This paper takes a novel approach to detect the latent currency portfolio of Chinese foreign exchange reserves and the underlying portfolio management strategies during 2000 and 2007. Based on a portfolio accounting identity and the budget constraint of the Chinese central bank's holding of foreign assets, the monthly growth rate of reserves can be decomposed into monthly rate of return, valuation effects of exchange rates, and monthly net purchase rate. The valuation effect reveals the value share of each currency. Bayesian inference is adopted to estimate the state‐space model with a mixture of Gaussian distributions. The results show that China significantly and dramatically diversified its reserves out of the US dollar in 2002: both the euro's value and quantity shares increased from 5% to more than 20%. By the end of 2007, China held about (at most) 67.3% of its reserves in the US dollar, 22% in the euro, 2.5% in the Japanese yen, 4.7% in the Australian dollar, and 3.5% in the British pound. The average annual rate of return was about 3%. Copyright © 2011 John Wiley & Sons, Ltd.
Protein conformation changes on block copolymer surfaces detected by antibody‐functionalized atomic force microscope tips
Authors: Palacio Manuel L. B. , Schricker Scott R. , Bhushan Bharat
Published: October 2011

Conformational changes of fibronectin (Fn) deposited on poly(methyl methacrylate) and poly(acrylic acid) block copolymers with identical chemical compositions were detected using an antibody‐functionalized atomic force microscope (AFM) tip. Based on the antibody‐protein adhesive force maps and phase imaging, it was found that the nanomorphology of the triblock copolymer is conducive to the exposure of the arginine‐glycine‐aspartic acid (RGD) groups in Fn. For the first time, X‐ray photoelectron spectroscopy was used to elucidate surface chemical composition and confirm AFM results. The findings demonstrate that block copolymer nanomorphology can be used to regulate protein conformation and potentially cellular response. © 2011 Wiley Periodicals, Inc. J Biomed Mater Res Part A:, 2012.
Chondrocyte redifferentiation in 3D: The effect of adhesion site density and substrate elasticity
Authors: Schuh Elena , Hofmann Sandra , Stok Kathryn , Notbohm Holger , Müller Ralph , Rotter Nicole
Published: October 2011

To obtain sufficient cell numbers for cartilage tissue engineering with autologous chondrocytes, cells are typically expanded in monolayer culture. As a result, they lose their chondrogenic phenotype in a process called dedifferentiation, which can be reversed upon transfer into a 3D environment. We hypothesize that the properties of this 3D environment, namely adhesion site density and substrate elasticity, would influence this redifferentiation process. To test this hypothesis, chondrocytes were expanded in monolayer and their phenotypical transition was monitored. Agarose hydrogels manipulated to give different RGD adhesion site densities and mechanical properties were produced, cells were incorporated into the gels to induce redifferentiation, and constructs were analyzed to determine cell number and extracellular matrix production after 2 weeks of 3D culture. The availability of adhesion sites within the gels inhibited cellular redifferentiation. Glycosaminoglycan production per cell was diminished by RGD in a dose‐dependent manner and cells incorporated into gels with the highest RGD density, remained positive for collagen type I and produced the least collagen type II. Substrate stiffness, in contrast, did not influence cellular redifferentiation, but softer gels contained higher cell numbers and ECM amounts after 2 weeks of culture. Our results indicate that adhesion site density but not stiffness influences the redifferentiation process of chondrocytes in 3D. This knowledge might be used to optimize the redifferentiation process of chondrocytes and thus the formation of cartilage‐like tissue. © 2011 Wiley Periodicals, Inc. J Biomed Mater Res Part A:, 2012.
Functionalization of reactive polymer multilayers with RGD and an antifouling motif: RGD density provides control over human corneal epithelial cell–substrate interactions
Authors: Tocce Elizabeth J. , Broderick Adam H. , Murphy Kaitlin C. , Liliensiek Sara J. , Murphy Christopher J. , Lynn David M. , Nealey Paul F.
Published: October 2011

Our study demonstrates that substrates fabricated using a “reactive” layer‐by‐layer approach promote well‐defined cell–substrate interactions of human corneal epithelial cells. Specifically, crosslinked and amine‐reactive polymer multilayers were produced by alternating “reactive” deposition of an azlactone‐functionalized polymer [poly(2‐vinyl‐4,4‐dimethylazlactone)] (PVDMA) and a primary amine‐containing polymer [branched poly(ethylene imine)] (PEI). Advantages of our system include a 5‐ to 30‐fold decrease in deposition time compared to traditional polyelectrolyte films and direct modification of the films with peptides. Our films react with mixtures of an adhesion‐promoting peptide containing Arg‐Gly‐Asp (RGD) and the small molecule D‐glucamine, a chemical motif which is nonfouling. Resulting surfaces prevent protein adsorption and promote cell attachment through specific peptide interactions. The specificity of cell attachment via immobilized RGD sequences was verified using both a scrambled RDG peptide control as well as soluble‐RGD competitive assays. Films were functionalized with monotonically increasing surface densities of RGD which resulted in both increased cell attachment and the promotion of a tri‐phasic proliferative response of a human corneal epithelial cell line (hTCEpi). The ability to treat PEI/PVDMA films with peptides for controlled cell–substrate interactions enables the use of these films in a wide range of biological applications. © 2011 Wiley Periodicals, Inc. J Biomed Mater Res Part A:, 2012.
Long-term impact of adherence to oral bisphosphonates on osteoporotic fracture incidence
Authors: Sampalis John S , Adachi Jonathan D , Rampakakis Emmanouil , Vaillancourt Julie , Karellis Angela , Kindundu Christian
Published: October 2011

Adherence to osteoporosis treatments is a critical parameter resulting in suboptimal effectiveness in real-life practice. The long-term effect of adherence on fracture risk has not been assessed. This was a retrospective study using provincial health insurance claims databases to assess the association between adherence to oral bisphosphonates (OBP) and incidence of osteoporotic fractures in all Ontario patients with osteoporosis between April 1996 and December 2009. Multivariate logistic regression models were used to assess the association between OBP adherence and fracture risk. Treatment duration was classified into 2-year intervals. Compliance was estimated with the medication possession ratio (MPR), and persistence was defined as the length of continuous therapy without a gap in refills >30 days. The study cohort was composed of 636,114 patients, among whom 36.1% were prescribed OBPs for 0 to 2 years, 19.7% for 2 to 4 years, 15.1% for 4 to 6 years, 12% for 6 to 8 years, 9.1% for 8 to 10 years, 6.1% for 10to 12 years, and 1.9% for 12 to 14 years. Overall, the mean (SD) compliance for the cohort was 0.72 (0.30) with 53.5% of the patients having compliance >80% and 24.6% being persistent with treatment during the 14-year follow-up period. Significant associations between high adherence and reduced fracture risk over the entire 14-year period were observed; the overall odds ratio for categorical compliance (MPR >80% or MPR ≤80%), continuous compliance, and persistence were 0.909 (95% confidence interval [CI] 0.893–0.925), 0.918 (95% CI 0.893–0.944), and 0.804 (95% CI 0.787–0.821), respectively. In conclusion, adherence to OBP in osteoporosis management is suboptimal in a real-life setting. A significant positive association exists between poor adherence and increased risk of osteoporotic fractures, which becomes augmented with longer treatment duration. © 2012 American Society for Bone and Mineral Research
Inhibition by zinc of deoxycholate‐induced apoptosis in HCT‐116 cells
Authors: Smith Abigail F. , Longpre Jennifer , Loo George
Published: October 2011

The bile acid, deoxycholate, can induce apoptosis although the effect of trace elements on such cell death is unknown. The aim of this study was to determine if deoxycholate‐induced apoptosis is influenced by zinc. HCT‐116 colon epithelial cells were pre‐treated with zinc and then exposed to deoxycholate. Membrane blebbing, formation of apoptotic bodies, and greater overall production of reactive oxygen species (ROS) occurred in cells exposed to deoxycholate, but zinc inhibited the occurrence of these three events caused by deoxycholate. Upon finer analysis, stimulation of mitochondrial superoxide production, mitochondrial dysfunction, and cytochrome c release were detected in cells exposed to deoxycholate, but zinc did not inhibit any of these three effects caused by deoxycholate. Additionally, caspase‐3 activation, plasma membrane phospholipid translocation, and also chromatin condensation and fragmentation were observed in cells exposed to deoxycholate, but all of these effects of deoxycholate, including the greater overall ROS production, were all inhibited by zinc. Because zinc did not prevent the three mitochondrial effects caused by deoxycholate, the last set of findings suggested that zinc hampered activation of an initiator caspase upstream of effector caspase‐3, in inhibiting deoxycholate‐induced HCT‐116 cell death. In examining this possibility, it was found that caspase‐8 activation caused by deoxycholate was blocked by zinc. Collectively, the results suggest that zinc can inhibit deoxycholate‐induced apoptotic cell death mediated by caspases. J. Cell. Biochem. 113: 650–657, 2012. © 2011 Wiley Periodicals, Inc.
First‐principle investigation of magnetic coupling mechanism in hypothesized A‐site‐ordered perovskite YMn3Sc4O12
Authors: Li Hongping , Lv Shuhui , Bai Yijia , Xia Yanjie , Liu Xiaojuan , Meng Jian
Published: October 2011

We have systematically investigated the electronic and magnetic properties of hypothesized A‐site‐ordered perovskite YMn3Sc4O12 using first‐principle calculation based on the density functional theory. Our calculated results predict that YMn3Sc4O12 is both thermodynamically and mechanically stable and its ground state is antiferromagnetic insulator. The Mn3+ is in the high‐spin state. More importantly, by comparison to YMn3Al4O12, we point out that the empty Sc 3d orbital provides the MnOScOMn superexchange interaction, which is similar to its isostructural perovskite CaCu3Ti4O12, and enhances the antiferromagnetic interaction between Mn ions. From these calculations, we can clearly see that the empty 3d orbital plays an important role to realize superexchange interaction. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
EXPLORING ACCOUNTABILITY DISCOURSES AND PRACTICES IN THE SPANISH AID SYSTEM
Authors: Boni Alejandra , Peris Jordi , McGee Rosemary , Acebillo‐Baqué Míriam , Hueso Andrés
Published: October 2011

This article aims to explore the different accountability discourses of the various actors in the Spanish international aid system and to examine them in light of the various theoretical interpretations of development accountability. The conclusions reached suggest a technical and financial accountability model, largely isolated from international debates where political and social issues are at the core of the concept. Although this can be explained by a range of factors which are specific to the Spanish aid system, there are also interesting tendencies that are deepening a new understanding and practice of the idea. Copyright © 2011 John Wiley & Sons, Ltd.
Synthesis and in vitro evaluation of 2‐[11C]methoxyestradiol‐3,17β‐O,O‐bissulfamate for in vivo studies of angiogenesis
Authors: Kang Choong Mo , Choe Yearn Seong , Jung Kyung‐Ho , Choi Joon Young , Lee Kyung‐Han , Kim Byung‐Tae
Published: October 2011

In the present study, 2‐methoxyestradiol‐3,17β‐O,O‐bissulfamate (1), a known angiogenesis inhibitor, was prepared in a radiolabeled form by 11C‐methylation of 2‐hydroxyestradiol‐3,17β‐O,O‐bis(N‐trityl)sulfamate (6) followed by detritylation. Synthesis of precursor 6 required a rather long step because of the presence of two sulfamoyl groups. The decay‐corrected radiochemical yield of [11C]1 was 19 ± 2% based on [11C]CH3I, and the specific activity was 34–39 GBq/µmol. Although 1 is known to significantly inhibit the proliferation of human umbilical vascular endothelial cells (HUVECs), its radiolabeled form, [11C]1 was not avidly taken up by HUVECs, and the uptake increased slightly in a time‐dependent manner (156% at 60 min relative to a value of 100% at 5 min). These results suggest that further studies are warranted to determine the molecular target for [11C]1. Copyright © 2011 John Wiley & Sons, Ltd.
High doses of salicylate and aspirin are inhibitory on acid‐sensing ion channels and protective against acidosis‐induced neuronal injury in the rat cortical neuron
Authors: Wang Wei , Ye Shan‐Dong , Zhou Ke‐Qing , Wu Li‐Min , Huang Yi‐Na
Published: October 2011

Aspirin and its main metabolite salicylate are widely used to relieve pain, treat inflammatory diseases, and prevent ischemic stroke. Multiple pathways are responsible for the therapeutic actions exerted by these drugs. One of the pathways is targeting neuronal receptors/ion channels in the central nervous system. Correspondingly, increasing evidence has implicated acid‐sensing ion channels (ASICs) in the processes of the diseases that are medicated by aspirin and salicylate. We therefore employed whole‐cell patch‐clamp recordings to examine the effects of salicylate as well as aspirin on ASICs in cultured cortical neurons of the rat. We recorded rapid and reversible inhibition of ASIC current by millimolar concentrations of aspirin and salicylate and found that salicylate reduced acidosis‐induced membrane depolarization. These data suggest that ASICs in the cortex are molecular targets of high doses of aspirin and salicylate. In addition, the results from lactate dehydrogenase release measurement showed that high doses of aspirin and salicylate protected the cortical neuron from acidosis‐induced neuronal injury. These findings may contribute to a better understanding of the therapeutic mechanisms of aspirin and salicylate actions in the brain and provide new evidence on aspirin and salicylate used as neuroprotective agents in the treatment of ischemic stroke. © 2011 Wiley Periodicals, Inc.
From an Epoxide Monomer Toolkit to Functional PEG Copolymers With Adjustable LCST Behavior
Authors: Mangold Christine , Obermeier Boris , Wurm Frederik , Frey Holger
Published: October 2011

The lower critical solution temperature (LCST) behavior of novel poly(ethylene glycol) (PEG)‐based copolymers bearing multiple functional groups, obtained by anionic ring‐opening (co)polymerization (AROP), has been investigated. Variable comonomer ratios of ethylene oxide (EO) and the corresponding oxiranes isopropylidene glyceryl glycidyl ether (IGG), ethoxyl vinyl glycidyl ether (EVGE), allyl glycidyl ether (AGE), or N,N‐dibenzyl amino glycidyl (DBAG), particularly designed to implement functional groups at the PEG backbone, were found to influence the LCST behavior. Sharp transitions from translucent to opaque solutions, comparable to other well‐established stimuli‐responsive polymers, were observed at temperatures ranging from 9 to 82 °C. The influence of the side group hydrophobicity could be quantified by the comparison of the different copolymer systems observed.
Genetic variability in DNA repair and cell cycle control pathway genes and risk of smoking‐related lung cancer
Authors: Buch Shama C. , Diergaarde Brenda , Nukui Tomoko , Day Roger S. , Siegfried Jill M. , Romkes Marjorie , Weissfeld Joel L.
Published: October 2011

DNA repair and cell cycle control play an important role in the repair of DNA damage caused by cigarette smoking. Given this role, functionally relevant single nucleotide polymorphisms (SNPs) in genes in these pathways may well affect the risk of smoking‐related lung cancer. We examined the relationship between 240 SNPs in DNA repair and cell cycle control pathway genes and lung cancer risk in a case–control study of white current and ex‐cigarette smokers (722 cases and 929 controls). Additive, dominant, and recessive genetic models were evaluated for each SNP. A genetic risk summary score was also constructed. Odds ratios (OR) for lung cancer risk and 95% confidence intervals (95% CI) were estimated using logistic regression models. Thirty‐eight SNPs were associated with lung cancer risk in our study population at P < 0.05. The strongest associations were observed for rs2074508 in GTF2H4 (Padditive = 0.003), rs10500298 in LIG1 (Precessive = 2.7 × 10−4), rs747658 and rs3219073 in PARP1 (rs747658: Padditive = 5.8 × 10−5; rs3219073: Padditive = 4.6 × 10−5), and rs1799782 and rs3213255 in XRCC1 (rs1799782: Pdominant = 0.006; rs3213255: Precessive = 0.004). Compared to individuals with first quartile (lowest) risk summary scores, individuals with third and fourth quartile summary score results were at increased risk for lung cancer (OR: 2.21, 95% CI: 1.66–2.95 and OR: 3.44, 95% CI: 2.58–4.59, respectively; Ptrend < 0.0001). Our data suggests that variation in DNA repair and cell cycle control pathway genes is associated with smoking‐related lung cancer risk. Additionally, combining genotype information for SNPs in these pathways may assist in classifying current and ex‐cigarette smokers according to lung cancer risk. © 2011 Wiley Periodicals, Inc.
PTBP1‐dependent regulation of USP5 alternative RNA splicing plays a role in glioblastoma tumorigenesis
Authors: Izaguirre Daisy I. , Zhu Wen , Hai Tao , Cheung Hannah C. , Krahe Ralf , Cote Gilbert J.
Published: October 2011

Aberrant RNA splicing is thought to play a key role in tumorigenesis. The assessment of its specific contributions is limited by the complexity of information derived from genome‐wide array‐based approaches. We describe how performing splicing factor‐specific comparisons using both tumor and cell line data sets may more readily identify physiologically relevant tumor‐specific splicing events. Affymetrix exon array data derived from glioblastoma (GBM) tumor samples with defined polypyrimidine tract‐binding protein 1 (PTBP1) levels were compared with data from U251 GBM cells with and without PTBP1 knockdown. This comparison yielded overlapping gene sets that comprised only a minor fraction of each data set. The identification of a novel GBM‐specific splicing event involving the USP5 gene led us to further examine its role in tumorigenesis. In GBM, USP5 generates a shorter isoform 2 through recognition of a 5′ splice site within exon 15. Production of the USP5 isoform 2 was strongly correlated with PTBP1 expression in GBM tumor samples and cell lines. Splicing regulation was consistent with the presence of an intronic PTBP1 binding site and could be modulated through antisense targeting of the isoform 2 splice site to force expression of isoform 1 in GBM cells. The forced expression of USP5 isoform 1 in two GBM cell lines inhibited cell growth and migration, implying an important role for USP5 splicing in gliomagenesis. These results support a role for aberrant RNA splicing in tumorigenesis and suggest that changes in relatively few genes may be sufficient to drive the process. © 2011 Wiley Periodicals, Inc.
New insights into the influence of cigarette smoking on urothelial carcinogenesis: Smoking‐induced gene expression in tumor‐free urothelium might discriminate muscle‐invasive from nonmuscle‐invasive urothelial bladder cancer
Authors: Gabriel Ute , Li Li , Bolenz Christian , Steidler Annette , Kränzlin Bettina , Saile Maria , Gretz Norbert , Trojan Lutz , Michel Maurice Stephan
Published: October 2011

Smoking is the main risk factor for urothelial bladder cancer. In former smokers the risk decreases but does not reach the low level of never smokers. This indicates reversible and permanent smoking‐derived genetic alterations. Transcriptional changes may point to mechanisms, how smoking promotes urothelial bladder cancer. To identify smoking‐derived transcriptional changes we performed gene expression profiling in current, former, and never smokers, using tumor and tumor‐free urothelium from patients with nonmuscle‐invasive urothelial bladder cancer (NMIBC) or muscle‐invasive urothelial bladder cancer (MIBC). Smoking turned out to influence gene expression much less than tumor stage (NMIBC or MIBC) and tumor transformation (tumor‐free or tumor). Smoking seemed to influence gene expression in patients with MIBC more strongly compared to those with NMIBC. The least irreversible changes after smoking cessation were proposed in tumor‐free urothelium from patients with NMIBC. Growth factors and oncogenes were up‐regulated in tumor‐free urothelium from smokers with MIBC but not from smokers with NMIBC. A panel of genes up‐regulated in smokers have potential for early detection and distinction of MIBC from NMIBC using tumor‐free tissue. © 2011 Wiley Periodicals, Inc.
“Kernkraftwerke sind keine Option für den Klimaschutz”
Authors: Nitsch Joachim
Published: October 2011

Der Ausstieg aus der Kernenergie in Deutschland ist ein kluger Schritt in Richtung des notwendigen raschen Strukturwandels in der Energieversorgung, findet Joachim Nitsch.
“Auch Kerntechnik kann eine Zukunftstechnologie sein”
Authors: Offermanns Heribert
Published: October 2011

Ein Wiederanfahren von Nuklearanlagen oder der Neubau von Reaktoren darf nicht ausgeschlossen werden, fordert Heribert Offermanns.
Akkreditierung im Wandel
Authors: Patscheke Heinrich
Published: October 2011

Aufgrund einer EU‐Verordnung gibt es seit 2010 in Deutschland nur noch eine Akkreditierungsagentur für Laboratorien, die Deutsche Akkreditierungsstelle Dakks. Kritik gibt es an ihrer Struktur, die sich inzwischen auch verändert hat, und an ihren Gebühren.
Chemical‐Driven Tissue Removal and Removal Profiles by Atmospheric Plasma Irradiation
Authors: Koo Il Gyo , Moore Cameron A. , Choi Myeong Yeol , Kim Gon Jun , Kim Paul Y. , Kim Yoon‐Sun , Yu Zengqi , Collins George J.
Published: October 2011

We demonstrate the application of RF‐excited plasma to remove localized regions of ex vivo tissue. While some limited tissue removal occurs when using discharges in rare gases alone, the addition of chemical precursors results in an enhancement of etch depth and etch profile under essentially identical plasma conditions of delivered power, applied voltage, and gas flow. Specifically, the material removal rate in our experiments using different CH4−xClx additives increased with both (i) the molecular chlorine content (x = 2,3,4) of the selected additive, and (ii) the concentration of haloalkane vapor in the gas stream. We attribute this enhancement to the generation and delivery of chemically reactive radicals from the plasma to the tissue, followed by formation of volatile products (i.e., a chemical, rather than physical or thermal, tissue removal process). In addition we observed that cross‐sectional etch profiles differed with the chosen haloalkane additive chemistries, indicative of corresponding differences in chemistries on profile side‐walls versus bottom walls.

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Plasma Deposition of Nanoscale Difluoromethylene Dominated Surfaces
Authors: Quade Antje , Schröder Karsten , Ohl Andreas , Weltmann Klaus‐Dieter
Published: October 2011

Polytetrafluoroethylene‐like coatings with a remarkably high amount of CF2 groups to the extent of 85% were deposited with a pulsed microwave discharge at low pressure. They were obtained by plasma enhanced chemical vapor deposition using solely octafluoropropane gas, C3F8, as precursor. The influence of gas pressure and microwave power on properties of the deposited coatings like content of CF2‐chains, F/C‐ratio, deposition rate, and wettability is described. Best results regarding a high difluoromethylene group content of the films were obtained at a pressure of 50 Pa at higher microwave powers. FTIR spectra show the two distinct absorption bands, which are assigned to the CF2 asymmetric and symmetric stretching modes, demonstrating convincingly the nature of the highly ordered PTFE‐like films.

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Atmospheric Pressure Plasma CVD of Amorphous Hydrogenated Silicon Carbonitride (a‐SiCN:H) Films Using Triethylsilane and Nitrogen
Authors: Guruvenket Srinivasan , Andrie Steven , Simon Mark , Johnson Kyle W. , Sailer Robert A.
Published: October 2011

Amorphous hydrogenated silicon carbonitride (a‐SiCN:H) thin films are synthesized by atmospheric pressure plasma enhanced chemical vapor (AP‐PECVD) deposition using the Surfx Atomflow™ 250D APPJ source with triethylsilane (HSiEt3, TES) and nitrogen as the precursor and the reactive gases, respectively. The effect of the substrate temperature (Ts) on the growth characteristics and the properties of a‐SiCN:H films was evaluated. The properties of the films were investigated via scanning electron microscopy (SEM), atomic force microscopy (AFM) for surface morphological analyses, Fourier transform infrared spectroscopy (FTIR), and X‐ray photoelectron spectroscopy (XPS) for chemical and compositional analyses; spectroscopic ellipsometry for optical properties and thickness determination and nanoindentation to determine the mechanical properties of the a‐SiCN:H films. Films deposited at low Ts depict organic like features, while the films deposited at high Ts depict ceramic like features. FTIR and XPS studies reveal that an increases in Ts helps in the elimination of organic moieties and incorporation of nitrogen in the film. Films deposited at Ts of 425 °C have an index of refraction (n) of 1.84 and hardness (H) of 14. 8 GPa. A decrease in the deposition rate between Ts of 25 and 250 °C and increase in deposition rate between Ts of 250 and 425 °C indicate that the growth of a‐SiCN:H films at lower Ts are surface reaction controlled, while at high temperatures film growth is mass‐transport controlled. Based on the experimental results, a potential route for film growth is proposed.

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Does Cross‐Link Density of PEO‐Like Plasma Polymers Influence their Resistance to Adsorption of Fibrinogen?
Authors: Choukourov Andrei , Gordeev Ivan , Arzhakov Dmitry , Artemenko Anna , Kousal Jaroslav , Kylián Ondřej , Slavínská Danka , Biederman Hynek
Published: October 2011

Thin films of PEO‐like plasma polymers with different extent of cross‐linking were deposited by plasma‐assisted vacuum thermal depolymerization of PEO. The films underwent considerable volume changes when in contact with water, i.e., they behaved as hydrogels. A Flory–Rehner theory of gels corrected for non‐Gaussian chain distribution was applied to derive the average molar mass between cross‐links. Films with up to ten monomeric units between cross‐links were fabricated, this number decreasing to one at enhanced rf power. Such changes of structure resulted in a three‐orders‐of‐magnitude increase of Young's modulus. Even highly cross‐linked films did not adsorb fibrinogen unless the concentration of the ether groups dropped below 65%.

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Study of roughness in multilayer Mo–Si mirrors
Authors: Valkovskiy G. A. , Baidakova M. V. , Brunkov P. N. , Konnikov S. G. , Yagovkina M. A. , Zadiranov Ju. M.
Published: October 2011

Combined approach based on X‐ray reflectometry (XRR), atomic‐force microscopy (AFM), and small‐angle X‐ray scattering (SAXS) has been applied to two series of multilayer Mo/Si mirrors grown by magnetron sputtering on standard and specially smoothed substrates under different technological conditions (A and B). Simulation of XRR data, using a model of two layers in period, can distinguish the mirror quality in terms of the total root mean square roughness. The quality is better for mirrors grown on smoother substrate, but it also depends on technological conditions. In addition, use of a model with transition layers reveals an asymmetry of Mo/Si and Si/Mo interfaces. Analysis of surface roughness PSD functions obtained by AFM shows that the surface diffusion is the dominant smoothing mechanism for all the mirrors studied. The low‐frequency roughness is conformal to that of the substrate for better mirrors (series A), but increases for poorer quality mirrors (series B). Simulation of SAXS data provides roughness parameters of the internal interfaces. For the better mirrors, the lateral correlation length of the roughness does not exceed 13 nm. However, this length is about 50 nm for the poorer quality mirrors, in agreement with AFM data.
Blending a probabilistic nowcasting method with a high‐resolution numerical weather prediction ensemble for convective precipitation forecasts
Authors: Kober K. , Craig G. C. , Keil C. , Dörnbrack A.
Published: October 2011

A seamless prediction of convective precipitation for a continuous range of lead times from 0–8 h requires the application of different approaches. Here, a nowcasting method and a high‐resolution numerical weather prediction ensemble are combined to provide probabilistic precipitation forecasts. For the nowcast, an existing deterministic extrapolation technique was modified by the local Lagrangian method to calculate the probability of exceeding a threshold value in radar reflectivity. Numerical forecasts were obtained from an experimental high‐resolution ensemble that provides 20 different deterministic forecasts of synthetic radar reflectivity. Probabilistic information was calculated by different approaches from the ensemble output. The probabilistic forecasts based on the ensemble were calibrated with the reliability diagram statistics method. The skill of the probabilistic nowcasts and forecasts was evaluated using three quality measures. Finally, a seamless probabilistic forecast was generated as an additive combination of nowcast and forecast, using a weighting function based on their relative skills. The skill of the seamless forecast was greater than or equal to that of the nowcast or ensemble forecast in all quality measures and at all lead times. Copyright © 2011 Royal Meteorological Society
ESTIMATION OF JUVENILE SALMON HABITAT IN PACIFIC RIM RIVERS USING MULTISCALAR REMOTE SENSING AND GEOSPATIAL ANALYSIS
Authors: Whited D. C. , Kimball J. S. , Lorang M. S. , Stanford J. A.
Published: October 2011

We conducted a regional classification and analysis of riverine floodplain physical features that represent key attributes of salmon rearing habitats. Riverine habitat classifications, including floodplain area and river channel complexity, were derived at moderate (30 m) spatial resolution using multispectral Landsat imagery and global terrain data (90 m) encompassing over 3 400 000 km2 and most North Pacific Rim (NPR) salmon rivers. Similar classifications were derived using finer scale (i.e. ≤ 2.4‐m resolution) remote sensing data over a smaller set of 31 regionally representative flood plains. A suite of physical habitat metrics (e.g. channel sinuosity, nodes, floodplain width) were derived from each dataset and used to assess the congruence between similar habitat features at the different spatial scales and to evaluate the utility of moderate scale geospatial data for determining abundance of selected juvenile salmon habitats relative to fine scale remote sensing measurements. The resulting habitat metrics corresponded favorably (p < 0.0001) between the moderate scale and the fine scale floodplain classifications; a subset of these metrics (channel nodes and maximum floodplain width) also were strong indicators (R2 > 0.5, p < 0.0001) of floodplain habitats defined from the finer scale analysis. These relationships were used to estimate the abundance and distribution of three critical shallow water floodplain habitats for juvenile salmon (parafluvial and orthofluvial springs, and shallow shore) across the entire NPR domain. The resulting database provides a potential tool to evaluate and prioritize salmon conservation efforts both within individual river systems and across major catchments on the basis of physical habitat distribution and abundance. Copyright © 2011 John Wiley & Sons, Ltd.
SEM of the tubules of the hepatopancreas and the stomach gland of the scorpion (buthus quinquestriatus): A methodological study
Authors: El‐Salhy M. , Grimalius L. , Arro E. , Fredriksson B. A. , Hörstedt P. , Brunk U.
Published: October 2011

Different procedures were tested for the purpose of circumventing the technical obstacles encountered in SEM of the scorpion hepatopancreas and stomach gland. These problems are caused by the relatively high osmotic pressure of the body fluid of this animal, the irregular surface contour, and the very high content of fat in the organs under investigation. The best results were obtained following glutaraldehyde fixation at an effective osmotic pressure approaching that of scorpion body fluid, ensuring stabilization of fat by post‐fixation in osmium tetroxide, and overcoming the charge effects via the OTOTO (Osmium‐Thiocarbohydrozide) method in combination with metal coating. Dehydration by CPD or FD both gave rise to inevitable artefacts (shrinkage or cracking). Used together, however, CPD and FD were complementary.

The surfaces of hepatopancreatic and stomach gland tubules showed a distinct similarity. Tubules of both organs were lined mostly with cells equipped with parallel arrays of microvilli on the apical surface and containing large amounts of fat.
Electron beam testing: Problems in practice
Authors: Wolfgang E.
Published: October 2011

Electron beam testing has now become an almost indispensable design verification aid for very large scale ICs. The test preparations for circuit analysis are very important as the purpose of these preparation is to ensure that the integrated circuit is driven as it was during characterization on the computerized test system. The same applies when the circuit is being irradiated by the electron beam. This involves the use of preparation techniques such as plasma etching and plasma cleaning, the development of measuring equipment, determining suitable parameters for the electron probe and constantly checking how the circuit is functioning. The actual circuit analysis is carried out in two stages – first the defective block is located and then the individual circuit responsible for the design weakness pinpointed. Cases may arise where measurements on interconnections covered by an oxide layer are required. It might also be necessary to impress signals on certain nodes using a mechanical probe or to separate the circuits.
Examples of image processing using a computer controlled SEM
Authors: Artz Bruce E.
Published: October 2011

Several examples of the use of digital image processing on SEM images are presented. The emphasis is on image enhancement as opposed to pattern recognition. Examples given include non‐linear histogram modification, noise filtering, and frame by frame subtraction. Image processing is done on digitally stored images obtained from a modified SEM. The SEM has been modified to allow minicomputer control of the electron/CRT beam position and blanking. Digitization of the sample signals, such as secondary electron, backscattered electron, and absorbed current is done using a 5 MHz voltage to frequency converter and a 100 KHz timer/sealer combination. Software for image storage and manipulation is also described.
Quantitative image and electron microprobe analysis
Authors: Beswick J. M.
Published: October 2011

Image analysis in the scanning electron microprobe analyser by use of a suitable digital scan drive/computer interface to an LSI 11/23 computer and dual 5.2 Mbyte hard disc system is described. The image processing of 1024 × 1024 pixel and 256 grey level resolution is performed to obtain size and particle coordinate positions. At these particle coordinates, x‐ray analysis is automatically performed by suitable interfacing to an EDAX PV 9100 EDX system. Software has been developed for electron microprobe analysis to interface with the spacial image analysis information. By use of the video range for binary image detections and correct choice of the elemental analysis parameters, composition specific image analysis of second phase features in microstructures can be obtained. The composition specific information can be expressed in terms of size related to composition range, or composition related to size range for up to 10 elements simultaneously.
A review of bone cell and substratum interactions: An illustration of the role of scanning electron microscopy
Authors: Jones S. J. , Boyde A. , Ali N. N. , Maconnachie E.
Published: October 2011

The first experimental studies concerning observations of changes in bone cell functional morphology were made using the SEM, and SEM has remained paramount in this field. Bone forming and resorbing cells only exist on surfaces – which are available for study after removal of adjacent tissue layers: The underlying matrix surface can then be studied after removal of the cells, and the mineral front examined after removing the matrix (with an appropriate solvent or by plasma ashing).

In this review, we analyse the main findings which we have made in this laboratory concerning the biological activities of osteoblasts (bone forming cells) and osteoclasts (bone resorbing cells). The technical problems of specimen preparation of cells which shrink more than the substrate to which they are attached have been convered previously (Boyde et al. 1977). Such problems obviously affect the lateral, cell to cell inter‐relationships more than the cell to substrate effects which we cover here.

At present, we can conclude that SEM has made a major contribution to bone biology by permitting observation of normal cells and natural and surrogate substrates. We confidently predict that it will continue to play a pivotal role in the closer observation of cell‐cell‐substrate interactions particularly in respect of local hormonal effects, as well as in bone pathology and implantology.
Methodology and practice of in situ differential scanning electron microscopy
Authors: Sicignano A. , Iravani M. Vaez
Published: October 2011

Contrast plays a crucial role both in qualitative and quantitative imaging in scanning microscopy. Usual methods of obtaining high contrast images in the scanning electron microscope (SEM) involve performing specific operations on the video signal already produced by the SEM. In this article, the concept of in situ differential imaging in the SEM is discussed. In this imaging modality, a true differential image of the sample is generated simultaneously with the normal video. The signal can be obtained at low and high video band‐widths, thus allowing low contrast objects to be readily imaged. Various methodologies developed to perform in situ differential imaging are reviewed. A characteristic of all these techniques is their sensitivity to edges, a feature which is extensively used in a number of applications. The ability to obtain feature enhancement in any desired direction is another important attribute of this approach. Examples are given on the use of the method in general imaging as well as in the metrology of critical dimensions.
A circuit for voltage coding synchronizing
Authors: Immediato M. J. , Jenkins K. A.
Published: October 2011

The appearance of stationary stripes in a voltage contrast SEM image of a circuit, generally known as voltage coding, is a commonly used technique for tracing circuit lines for failure analysis and for locating nodes for waveform measurements. Maintaining a steady striped image requires synchronizing a pattern generator to the SEM raster scan. A circuit is described which can be attached to any SEM to perform this synchronization, and which has a number of features which extend the usefulness of voltage coding.
A glimpse into the future: Automatic recognition of elusive structures in the electron microscope
Authors: Hawkes P.W.
Published: October 2011

Attention is drawn to the possible advantages of using grammatical methods of feature description in electron microscopy.
A new high‐resolution dual‐probe system for detecting and imaging thermal and plasma waves
Authors: Suddendorf M. B. , Liu M. , Somekh M. G.
Published: October 2011

Thermal and plasma waves have been simultaneously and independently probed by a novel differential system. This new detection system for characterising and imaging materials such as semiconductors in a noncontacting, nondestructive manner, is based on two parallel, heterodyne interferometers, which probe the specimen on a microscopic scale. These detect changes in sample reflectivity and surface displacement which are induced by a separate laser source. The optical and electronic configuration is described and results showing the measurement and imaging capabilities of the system are presented. New results indicating interference between photodisplacement and photoreflectance effects are discussed.
Gaussian‐based routines to impute categorical variables in health surveys
Authors: Yucel Recai M. , He Yulei , Zaslavsky Alan M.
Published: October 2011

The multivariate normal (MVN) distribution is arguably the most popular parametric model used in imputation and is available in most software packages (e.g., SAS PROC MI, R package norm). When it is applied to categorical variables as an approximation, practitioners often either apply simple rounding techniques for ordinal variables or create a distinct ‘missing’ category and/or disregard the nominal variable from the imputation phase. All of these practices can potentially lead to biased and/or uninterpretable inferences. In this work, we develop a new rounding methodology calibrated to preserve observed distributions to multiply impute missing categorical covariates. The major attractiveness of this method is its flexibility to use any ‘working’ imputation software, particularly those based on MVN, allowing practitioners to obtain usable imputations with small biases. A simulation study demonstrates the clear advantage of the proposed method in rounding ordinal variables and, in some scenarios, its plausibility in imputing nominal variables. We illustrate our methods on a widely used National Survey of Children with Special Health Care Needs where incomplete values on race posed a valid threat on inferences pertaining to disparities. Copyright © 2011 John Wiley & Sons, Ltd.
The optimal discovery procedure in multiple significance testing: an empirical Bayes approach
Authors: Noma Hisashi , Matsui Shigeyuki
Published: October 2011

Multiple testing has been widely adopted for genome‐wide studies such as microarray experiments. To improve the power of multiple testing, Storey (J. Royal Statist. Soc. B 2007; 69: 347–368) recently developed the optimal discovery procedure (ODP) which maximizes the number of expected true positives for each fixed number of expected false positives. However, in applying the ODP, we must estimate the true status of each significance test (null or alternative) and the true probability distribution corresponding to each test. In this article, we derive the ODP under hierarchical, random effects models and develop an empirical Bayes estimation method for the derived ODP. Our methods can effectively circumvent the estimation problems in applying the ODP presented by Storey. Simulations and applications to clinical studies of leukemia and breast cancer demonstrated that our empirical Bayes method achieved theoretical optimality and performed well in comparison with existing multiple testing procedures. Copyright © 2011 John Wiley & Sons, Ltd.