bluuebunny/crossref_metadata_2025 huggingface dataset:
Alternation of extracellular matrix remodeling and apoptosis by activation of the aryl hydrocarbon receptor pathway in human periodontal ligament cells
Authors: Tomokiyo Atsushi , Maeda Hidefumi , Fujii Shinsuke , Monnouchi Satoshi , Wada Naohisa , Hori Kiyomi , Koori Katsuaki , Yamamoto Naohide , Teramatsu Yoko , Akamine Akifumi
Published: May 2012

It is well known that the aryl hydrocarbon receptor (AhR) is involved in the toxicity of halogenated aromatic hydrocarbons (HAH) and polycyclic aromatic hydrocarbons (PAH). Recent experiments have shown the induction of impaired tooth and hard‐tissue formation by AhR pathway activation, however, the effect on periodontal ligament (PDL) tissue remains unclear. Here, we investigated the effects of benzo(a)pyrene (BaP), a member of PAH, on the extracellular matrix (ECM) remodeling‐related molecules, collagen type I (COL‐I), matrix metalloproteinase‐1 (MMP‐1), alpha‐smooth muscle actin (α‐SMA) expression, and apoptosis in two different human periodontal ligament cells (HPDLCs). The transduction of AhR from the cytoplasm to the nucleus and the increase of AhR‐responsive genes; that is, cytochrome P450 1A1 (CYP1A1), cytochrome P450 1B1 (CYP1B1), and aryl‐hydrocarbon receptor repressor (AhRR), expression was induced by BaP exposure in both HPDLCs. BaP treatment significantly enhanced MMP‐1 mRNA expression and MMP‐1 protein production, while markedly suppressing COL‐I and a‐SMA mRNA expression in both HPDLCs. Furthermore, these BaP‐treated HPDLCs fell into apoptotic cell death as evidenced by induction in annexin V and caspase‐3/7 staining and reduction of total cell number and Bcl‐2 mRNA expression. Thus, BaP exposure altered the expression of ECM‐related molecules and induced apoptosis in HPDLCs through activation of the AhR pathway. Overactivity of the AhR pathway may induce an inappropriate turnover of PDL tissue via disordered ECM remodeling and apoptosis in PDL cells. J. Cell. Biochem. 113: 3093–3103, 2012. © 2012 Wiley Periodicals, Inc.
Enhanced saccharification of corn straw pretreated by alkali combining crude ligninolytic enzymes
Authors: Li Jiang , Sun Fenghui , Li Xiangzhen , Yan Zhiying , Yuan Yuexiang , Liu XiaoFeng
Published: May 2012

BACKGROUND: This work investigated the monokaryogenesis of dikaryon strains of Trametes hirsuta by protoplasts regeneration for extracellular ligninolytic enzyme production. Saccharification of corn straw was enhanced by alkali pretreatment combining crude ligninolytic enzymes.

RESULTS: Effectiveness of alkali pretreatment of corn straw on delignification was evaluated under different concentrations. About 45% lignin loss was achieved at the concentration of 1.5% NaOH. In addition, 79.0% sugar yield was obtained after combined pretreatment with NaOH and crude ligninolytic enzyme produced from monokaryotic strains of Trametes hirsuta. Scanning electron microscopy (SEM) images showed that the porosity and surface area increased significantly after combined pretreatment. The FTIR spectra indicated that great intensity changes occurred at the 890–900 cm−1, 1509–1513 cm−1 and 1595 cm−1 bands.

CONCLUSION: The proposed combined pretreatment removes lignin and enhances saccharification of corn straw effectively. Copyright © 2012 Society of Chemical Industry
Intraabdominal extrapulmonary sequestration diagnosed by color doppler ultrasound at 22 weeks' gestation
Authors: Adaletli Ibrahim , Uludag Seyfettin
Published: May 2012

Intraabdominal extrapulmonary sequestration is seen very rarely. When a left suprarenal mass is detected in prenatal sonography, vascularization of the lesion should be evaluated with color Doppler sonography. We present a case of intraabdominal extrapulmonary sequestration that was diagnosed by color Doppler ultrasound at 22 weeks' gestation. © 2012 Wiley Periodicals, Inc. J Clin Ultrasound, 2013
Perihepatic abscess caused by dropped appendicoliths following laparoscopic appendectomy: Sonographic findings
Authors: Black Michelle T. , Ha Bo Yoon , Kang Young S. , Garland Adella M.
Published: May 2012

We report the case of a 6‐year‐old girl presenting with acute appendicitis complicated by perforated appendix, followed by perihepatic abscess associated with ectopic appendicoliths. CT findings were initially suspicious for an intrahepatic abscess with internal calcifications. However, on sonography the abscess appeared to be in a perihepatic location. Perihepatic abscess associated with a dropped or retained appendicolith has been rarely reported. Awareness of the possibility of a perihepatic abscess as a complication of laparoscopic appendectomy and use of sonography should result in optimal management of this rare complication. © 2012 Wiley Periodicals, Inc. J Clin Ultrasound 41:366–369, 2013
An unusual case of myocardial noncompaction involving both ventricles—Case report
Authors: Pradhan Dipesh , Liping Chen , Jian Sun , Karki Sanjaya , Abdoulwahabi David , Dewan Himalaya
Published: May 2012

Noncompaction of ventricular myocardium (NCVM) is a rare congenital cardiomyopathy characterized by numerous excessively prominent trabeculations and intertrabecular recesses in the myocardium without any other cardiac structural abnormality. Transthoracic echocardiography is the imaging modality of choice for diagnosing NCVM. Although this disease commonly affects the left ventricle, the right ventricle or both ventricles can rarely be affected. We report the case of an 18‐year‐old male patient with NCVM involving both ventricles. © 2012 Wiley Periodicals, Inc. J Clin Ultrasound 41:389–391, 2013
Single agent‐ and combination treatment with two targeted suicide gene therapy systems is effective in chemoresistant small cell lung cancer cells
Authors: Michaelsen Signe R. , Christensen Camilla L. , Sehested Maxwell , Cramer Frederik , Poulsen Thomas T. , Patterson Adam V. , Poulsen Hans S.
Published: May 2012

Background

Transcriptional targeted suicide gene (SG) therapy driven by the insulinoma‐associated 1 (INSM1) promoter makes it possible to target suicide toxin production and cytotoxicity exclusively to small cell lung cancer (SCLC) cells and tumors. It remains to be determined whether acquired chemoresistance, as observed in the majority of SCLC patients, desensitizes SCLC cells to INSM1 promoter‐driven SG therapy.

Methods

A panel of SCLC cell lines resistant to clinically relevant chemotherapeutics was characterized regarding the expression of proteins involved in response to chemotherapy and regarding INSM1 promoter activity. Sensitivity towards INSM1 promoter‐driven SG therapy was tested using different systems: Yeast cytosine deaminase‐uracil phosphoribosyl transferase (YCD‐YUPRT) in combination with the prodrug 5‐fluorocytosine (5‐FC) or Escherichia coli nitroreductase (NTR) together with the bromomustard prodrug SN27686.

Results

The chemoresistant cell lines displayed heterogeneous expression profiles of molecules involved in multidrug resistance, apoptosis and survival pathways. Despite this, the INSM1 promoter activity was found to be unchanged or increased in SCLC chemoresistant cells and xenografts compared to chemosensitive variants. INSM1 promoter‐driven SG therapy with YCD‐YUPRT/5‐FC or NTR/SN27686, was found to induce high levels of cytotoxicity in both chemosensitive and chemoresistant SCLC cells. Moreover, the combination of INSM1 promoter‐driven YCD‐YUPRT/5‐FC therapy and chemotherapy, as well as the combination of INSM1 promoter‐driven YCD‐YUPRT/5‐FC and NTR/SN27686 therapy, was observed to be superior to single agent therapy in chemoresistant SCLC cells.

Conclusions

Collectively, the present study demonstrates that targeted SG therapy is a potent therapeutic approach for chemoresistant SCLC patients, with the highest efficacy achieved when applied as combination SG therapy or in combination with standard chemotherapy. Copyright © 2012 John Wiley & Sons, Ltd.
Repetition and Reconfiguration: Demand‐Based Confabulation in Initial Eyewitness Memory
Authors: Sharps Matthew J. , Herrera Megan , Dunn Laurel , Alcala Emanuel
Published: May 2012

Repeated recall, as a result of repeated questioning, is typical of situations involving eyewitness evidence. The present study addressed questions of eyewitness performance with reference to repeated questioning in an initial interview, in a format based on actual police procedures. This experiment focused on eyewitness accuracy, eyewitness confidence, and the addition of false details to eyewitness accounts. Ninety‐two adult respondents were asked to recall all the information they could from a single viewing of a scene depicting an assailant aiming a handgun at a victim. This initial question was followed by three additional questions, in which respondents were asked to report any additional details they could recall. On average, respondents provided several times as many correct as false details to the initial question. However, performance deteriorated significantly to the three subsequent questions; on average, across the three subsequent questions, witnesses recalled nearly as much false as accurate information. Witness confidence was positively related to amount of accurate information recalled. However, confidence was also positively related to the number of instances of erroneous recall. These results indicate that reconfigurative dynamics begin to operate, producing confabulated responses in response to questioning demands, as early as the initial interview. This work may also help to clarify the critical relationship between accuracy and confidence in eyewitness reportage, at least within the framework reflected by the present research. Copyright © 2012 John Wiley & Sons, Ltd.
MR spectroscopic imaging and diffusion‐weighted imaging of prostate cancer with Gleason scores
Authors: Nagarajan Rajakumar , Margolis Daniel , Raman Steven , Sarma Manoj K. , Sheng Ke , King Christopher R. , Verma Gaurav , Sayre James , Reiter Robert E. , Thomas M. Albert
Published: May 2012

Purpose:

To investigate functional changes in prostate cancer patients with three pathologically proven different Gleason scores (GS) (3+3, 3+4, and 4+3) using magnetic resonance spectroscopic imaging (MRSI) and diffusion‐weighted imaging (DWI).

Materials and Methods:

In this study MRSI and DWI data were acquired in 41 prostate cancer patients using a 1.5T MRI scanner with a body matrix combined with an endorectal coil. The metabolite ratios of (Cho+Cr)/Cit were calculated from the peak integrals of total choline (Cho), creatine (Cr), and citrate (Cit) in MRSI. Apparent diffusion coefficient (ADC) values were derived from DWI for three groups of Gleason scores. The sensitivity and specificity of MRSI and DWI in patients were calculated using receiver operating characteristic curve (ROC) analysis.

Results:

The mean and standard deviation of (Cho+Cr)/Cit ratios of GS 3+3, GS 3+4, and GS 4+3 were: 0.44 ± 0.02, 0.56 ± 0.06, and 0.88 ± 0.11, respectively. For the DWI, the mean and standard deviation of ADC values in GS 3+3, GS 3+4, and GS 4+3 were: 1.13 ± 0.11, 0.97 ± 0.10, and 0.83 ± 0.08 mm2/sec, respectively. Statistical significances were observed between the GS and metabolite ratio as well as ADC values and GS.

Conclusion:

Combined MRSI and DWI helps identify the presence and the proportion of aggressive cancer (ie, Gleason grade 4) that might not be apparent on biopsy sampling. This information can guide subsequent rebiopsy management, especially for active surveillance programs. J. Magn. Reson. Imaging 2012;36:697–703. © 2012 Wiley Periodicals, Inc.
An online nano‐LC‐ESI‐FTICR‐MS method for comprehensive characterization of endogenous fragments from amyloid β and amyloid precursor protein in human and cat cerebrospinal fluid
Authors: Brinkmalm Gunnar , Portelius Erik , Öhrfelt Annika , Mattsson Niklas , Persson Rita , Gustavsson Mikael K. , Vite Charles H. , Gobom Johan , Månsson Jan‐Eric , Nilsson Jonas , Halim Adnan , Larson Göran , Rüetschi Ulla , Zetterberg Henrik , Blennow Kaj , Brinkmalm Ann
Published: May 2012

Amyloid precursor protein (APP) is the precursor protein to amyloid β (Aβ), the main constituent of senile plaques in Alzheimer's disease (AD). Endogenous Aβ peptides reflect the APP processing, and greater knowledge of different APP degradation pathways is important to understand the mechanism underlying AD pathology. When one analyzes longer Aβ peptides by low‐energy collision‐induced dissociation tandem mass spectrometry (MS/MS), mainly long b‐fragments are observed, limiting the possibility to determine variations such as amino acid variants or post‐translational modifications (PTMs) within the N‐terminal half of the peptide. However, by using electron capture dissociation (ECD), we obtained a more comprehensive sequence coverage for several APP/Aβ peptide species, thus enabling a deeper characterization of possible variants and PTMs.

Abnormal APP/Aβ processing has also been described in the lysosomal storage disease Niemann–Pick type C and the major large animal used for studying this disease is cat. By ECD MS/MS, a substitution of Asp7 → Glu in cat Aβ was identified. Further, sialylated core 1 like O‐glycans at Tyr10, recently discovered in human Aβ (a previously unknown glycosylation type), were identified also in cat cerebrospinal fluid (CSF). It is therefore likely that this unusual type of glycosylation is common for (at least) species belonging to the magnorder Boreoeutheria. We here describe a detailed characterization of endogenous APP/Aβ peptide species in CSF by using an online top‐down MS‐based method. Copyright © 2012 John Wiley & Sons, Ltd.
Analysis of lipids with desorption atmospheric pressure photoionization‐mass spectrometry (DAPPI‐MS) and desorption electrospray ionization‐mass spectrometry (DESI‐MS)
Authors: Suni Niina M. , Aalto Henni , Kauppila Tiina J. , Kotiaho Tapio , Kostiainen Risto
Published: May 2012

In this article, the effect of spray solvent on the analysis of selected lipids including fatty acids, fat‐soluble vitamins, triacylglycerols, steroids, phospholipids, and sphingolipids has been studied by two different ambient mass spectrometry (MS) methods, desorption electrospray ionization‐MS (DESI‐MS) and desorption atmospheric pressure photoionization‐MS (DAPPI‐MS). The ionization of the lipids with DESI and DAPPI was strongly dependent on the spray solvent. In most cases, the lipids were detected as protonated or deprotonated molecules; however, other ions were also formed, such as adduct ions (in DESI), [M‐H]+ ions (in DESI and DAPPI), radical ions (in DAPPI), and abundant oxidation products (in DESI and DAPPI). DAPPI provided efficient desorption and ionization for neutral and less polar as well as for ionic lipids but caused extensive fragmentation for larger and more labile compounds because of a thermal desorption process. DESI was more suitable for the analysis of the large and labile lipids, but the ionization efficiency for less polar lipids was poor. Both methods were successfully applied to the direct analysis of lipids from pharmaceutical and food products. Although DESI and DAPPI provide efficient analysis of lipids, the multiple and largely unpredictable ionization reactions may set challenges for routine lipid analysis with these methods. Copyright © 2012 John Wiley & Sons, Ltd.
Formation of positive cluster ions LinBr (n = 2–7) and ionization energies studied by thermal ionization mass spectrometry
Authors: Veličković S. R. , Đustebek J. B. , Veljković F. M. , Veljković M. V.
Published: May 2012

Clusters of the type LinX (X = halides) can be considered as potential building blocks of cluster‐assembly materials. In this work, LinBr (n = 2–7) clusters were obtained by a thermal ionization source of modified design and selected by a magnetic sector mass spectrometer. Positive ions of the LinBr (n = 4–7) cluster were detected for the first time. The order of ion intensities was Li2Br+ > Li4Br+ > Li5Br+ > Li6Br+ > Li3Br+. The ionization energies (IEs) were measured and found to be 3.95 ± 0.20 eV for Li2Br, 3.92 ± 0.20 eV for Li3Br, 3.93 ± 0.20 eV for Li4Br, 4.08 ± 0.20 eV for Li5Br, 4.14 ± 0.20 eV for Li6Br and 4.19 ± 0.20 eV for Li7Br. All of these clusters have a much lower ionization potential than that of the lithium atom, so they belong to the superalkali class. The IEs of LinBr (n = 2–4) are slightly lower than those in the corresponding small Lin or LinH clusters, whereas the IEs of LinBr are very similar to those of Lin or LinH for n = 5 and 6.

The thermal ionization source of modified design is an important means for simultaneously obtaining and measuring the IEs of LinBr (n = 2–7) clusters (because their ions are thermodynamically stable with respect to the loss of lithium atoms in the gas phase) and increasingly contributes toward the development of clusters for practical applications. Copyright © 2012 John Wiley & Sons, Ltd.
Perforated dried blood spot accurate microsampling: the concept and its applications in toxicokinetic sample collection
Authors: Li Fumin , Ploch Stephen , Fast Douglas , Michael Steve
Published: May 2012

Dried blood spot (DBS) sampling has gained considerable interest as a microsampling technique to support drug discovery and development owing to its enormous ethical and practical benefits. Quantitative determinations of drugs and/or their metabolites collected in DBS matrix in its current format, however, have encountered technical challenges and regulatory uncertainty. The challenges of DBS bioanalysis are largely ascribed to the way how samples are collected and analyzed. Currently, an uncontrolled amount of a blood sample, e.g. 20 µl, is collected per time point per sample and spotted onto cellulose paper. Quantitation is based on removal of a fixed area of the DBS sample, resulting in sample waste, a need for mechanical punching and concomitant potential punching carryover, uncertainty in recovery assessment and the adverse impact of hematocrit on accurate quantitation. Here, we describe the concept and applications of a novel concept, namely perforated dried blood spot (PDBS), for accurate microsampling that addresses previous challenges. Advantages of PDBS are enumerated and compared with conventional DBS in the context of microsampling and liquid chromatography tandem mass spectrometry bioanalysis. Two approaches for accurate microsampling of a small volume of blood (5 µl) are proposed and demonstrated, i.e. Microsafe® pipettes and the Drummond incremental pipette. Two online sample enrichment techniques to enhance liquid chromatography tandem mass spectrometry sensitivity for microsampling bioanalysis are discussed. The PDBS concept was successfully applied for accurate sample collection (5 µl) in a toxicokinetic study in rats given a single oral gavage dose of acetaminophen. Perspectives on bioanalytical method validation for regulated DBS/PDBS microsampling are also presented. Copyright © 2012 John Wiley & Sons, Ltd.
Pleistocene biogeochemical record in the south‐west Pacific Ocean (images site MD97‐2114, Chatham Rise)
Authors: Cobianchi M. , Luciani V. , Lupi C. , Mancin N. , Lirer F. , Pelosi N. , Trattenero I. , Bordiga M. , Hall I. R. , Sprovieri M.
Published: May 2012

Through a multidisciplinary approach based on novel micropaleontological and geochemical analyses, the main paleoceanographic and paleoclimate changes that have influenced the surface‐ and deep‐water circulation in the SW Pacific Ocean (Chatham Rise, eastern New Zealand) during the last million years are reconstructed. This region represents a key area for investigating the climate evolution during the Pleistocene because here the largely wind‐driven Antarctic Circumpolar Current interacts with the west Pacific Ocean circulation via the Deep Western Boundary Current, the major source of deep water for the whole Pacific Ocean. To understand coupling or decoupling events between sea surface and bottom waters, a continuous marine sedimentary succession since 1.1 Ma, recovered by the IMAGES (International Marine Past Global Change Study) cruise in the SW Pacific Ocean (Core MD97‐2114), has been investigated based on calcareous planktonic and benthic microfossil content and C and O isotope record performed on planktonic and benthic foraminiferal tests. Results show the occurrence of long‐ and short‐term patterns of climate and ocean circulation in the last million years as the result of the interplay of ice‐sheet dynamics, surface tropical versus polar water inflow, and trophic status of the surface water. Copyright © 2012 John Wiley & Sons, Ltd.
Deglaciation and catchment ontogeny in coastal south‐west Greenland: implications for terrestrial and aquatic carbon cycling
Authors: Leng Melanie J. , Wagner Bernd , Anderson N. John , Bennike Ole , Woodley Ewan , Kemp Simon J.
Published: May 2012

Here we present Holocene organic carbon, nitrogen, sulphur, carbon isotope ratio and macrofossil data from a small freshwater lake near Sisimiut in south‐west Greenland. The lake was formed c. 11 cal ka BP following retreat of the ice sheet margin and is located above the marine limit in this area. The elemental and isotope data suggest a complex deglaciation history of interactions between the lake and its catchment, reflecting glacial retreat and post‐glacial hydrological flushing probably due to periodic melting of local remnant glacial ice and firn areas between 11 and 8.5 cal ka BP. After 8.5 cal ka BP, soil development and associated vegetation processes began to exert a greater control on terrestrial–aquatic carbon cycling. By 5.5 cal ka BP, in the early Neoglacial cooling, the sediment record indicates a change in catchment–lake interactions with consistent δ13C while C/N exhibits greater variability. The period after 5.5 cal ka BP is also characterized by higher organic C accumulation in the lake. These changes (total organic carbon, C/N, δ13C) are most likely the result of increasing contribution (and burial) of terrestrial organic matter as a result of enhanced soil instability, as indicated by an increase in Cenococcum remains, but also Sphagnum and Empetrum. The impact of glacial retreat and relatively subdued mid‐ to late Holocene climate variation at the coast is in marked contrast to the greater environmental variability seen in inland lakes closer to the present‐day ice sheet margin. Copyright © 2012 John Wiley & Sons, Ltd.
A late Holocene climate record in stalagmites from Modrič Cave (Croatia)
Authors: Rudzka D. , Mcdermott F. , Surić M.
Published: May 2012

Few terrestrial Holocene climate records exist from south‐eastern Europe despite its important geographical position as a transitional climatic zone between the Mediterranean and mainland continental Europe. Here we present new petrographic and stable isotope data for two Holocene speleothems from Modrič Cave, Croatia (44°15′N, 15°32′E), a coastal Adriatic site (120 m inland). Modern meteorological and cave conditions have been monitored for 2 years to understand the links between climate variability and stable isotope time‐series records in speleothems. Typical of a Mediterranean‐type climate, a negative water balance exists between April and September, so that recharge of the aquifer is restricted to the winter months. The weighted mean δ18O of the rainfall is −5.96‰ (2σ = 2.83), and the weighted mean D/H rainfall value is −36.83‰ (2σ = 19.95), slightly above the Global Meteoric Water Line, but well below the Mediterranean Meteoric Water Line. Modern calcite from the tops of each stalagmite exhibits δ18O values that are close to isotopic equilibrium with their respective drip water values. Unfortunately, the relatively young ages and low uranium contents (ca. 50 p.p.b.) of both stalagmites hamper the use of U‐series dating. Radiocarbon dates have been used instead to constrain their chronology using a dead carbon correction. Apart from some Isotope Stage 3 material (ca. 55 ka), both stalagmites were deposited during the late Holocene. Climatic conditions during the late Holocene are inferred to have been sufficiently wet to maintain stalagmite growth and any hiatuses appear to be relatively short lived. Inferred changes in the stalagmite diameters during deposition are linked to δ13C and δ18O variations, indicating alternating periods of drier and wetter conditions. Drier conditions are inferred for the late Roman Ages warm period and the mid‐Medieval Warm Period. Wetter conditions are associated with the Little Ice Age. Copyright © 2012 John Wiley & Sons, Ltd.
Preparation of immunomodulatory hydrolysates from Alaska pollock frame
Authors: Hou Hu , Fan Yan , Li Bafang , Xue Changhu , Yu Guangli
Published: May 2012

BACKGROUND: Immunomodulatory peptides can enhance body immunity. There have been few systematic investigations on preparing immunomodulatory peptides from Alaska pollock frame. The aim of this study was to obtain such peptides from Alaska pollock frame and determine their properties.

RESULTS: Trypsin protein hydrolysate (TPH) significantly enhanced the proliferation of spleen lymphocytes, T cells and peritoneal macrophages (P < 0.05). Compared with TPH with molecular weight (MW) > 2 kDa, TPH with MW < 2 kDa showed higher lymphocyte proliferation activity at 10, 50 and 500 µg ml−1. The optimised hydrolysis conditions were a temperature of 50 °C, an enzyme dose of 24 U mg−1 and a time of 290 min. The proliferation rate and degree of hydrolysis were 28.45 ± 1.79% and 16.87 ± 0.15% respectively. The main amino acids in TPH were proline, aspartate, glutamic acid and leucine. TPH had high solubility and low viscosity. TPH showed high stability under both acid and alkaline conditions or when digested by trypsin and/or pepsin.

CONCLUSION: TPH showed high immunomodulatory activity, with molecular weight and amino acid composition being the important factors affecting this activity. TPH had high solubility, low viscosity and high stability. As a good immunomodulator, TPH may therefore have wide application. Copyright © 2012 Society of Chemical Industry
Nanocomposite p‐n Junction Polycarbazole CdSe/TiO2 Thin Films on ITO via Electrochemical Crosslinking
Authors: Frau Antonio F. , Park Yushin , Pernites Roderick B. , Advincula Rigoberto C.
Published: May 2012

The fabrication and characterization of a hybrid polymer p‐n junction‐type thin film via electropolymerization of NPs and a precursor polymer is described. Blends of TiO2 NPs, CdSe NCs, Cbz‐COOH, and PVK were utilized to enable electrochemical deposition on ITO glass substrates. Spectroscopic, microscopic, and wetting measurements confirmed thin film fabrication. CV yielded a CPN nanocomposite with electropolymerized (i.e., crosslinked) carbazole units embedding CdSe NCs. Absorption and emission measurements confirmed a charge transfer mechanism between the crosslinked carbazole and the NCs resulting in a p‐n junction‐type thin film on ITO; with the observed quenching of CdSe NC emission. Several possible applications of such thin films are also discussed.

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The Role of a Nanoscale Interphase from Plasma Polymers on the Micromechanics of Fiber Composites
Authors: Photjanataree Penchom , Liu Zheng , Jones Frank Ralph
Published: May 2012

A model composite is used to simulate the interphase between an allylamine/1,7‐octadiene plasma copolymer‐coated fiber and an epoxy resin. Time‐of‐flight secondary‐ion mass spectrometry (ToF‐SIMS) is used to identify the structure of the interacting polymers and the locus of failure. The crack propagates near to one of the glass surfaces where a bonded semi‐interpenetrating network forms. The effect of functionality of the plasma copolymer coating (or size) and its thickness on interfacial stress transfer efficiency (STE) at a fiber‐break is studied using the fragmentation test. The cumulative stress transfer function and associated STE is able to differentiate between the improvement with increasing amine group concentration and decreasing thickness of the plasma polymer.

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Carbon Fibers: Precursors, Manufacturing, and Properties
Authors: Frank Erik , Hermanutz Frank , Buchmeiser Michael R.
Published: May 2012

The properties, structure, and processing of carbon fibers are reviewed. Carbon fibers are made from several precursors, with PAN being the dominating precursor in the market. Carbon fibers have high tensile strength, high modulus (up to the theoretical limit of around 1000 GPa), and low density, depending on the structure and processing in very limited combinations. Both the structure and composition of the precursor affect the properties of the resulting carbon fibers significantly. Although the essential processes for carbon fiber production are similar, different precursors require different processing conditions in order to achieve improved performance. Future developments are discussed.

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Traces of Orlicz‐Sobolev functions under general growth restrictions
Authors: Kałamajska Agnieszka , Krbec Miroslav
Published: May 2012

We prove an estimate for the trace operator in spaces whose weak derivatives are in Orlicz spaces without constraints upon the growth of the generating Young function. This extends the known trace theorems established in Orlicz‐Sobolev spaces, where the complementary Young function had to fulfill the Δ2‐condition.
Microencapsulation of a Crop Protection Compound by Initiated Chemical Vapor Deposition
Authors: Bose Ranjita K. , Heming Alex M. , Lau Kenneth K. S.
Published: May 2012

In this work, initiated chemical vapor deposition (iCVD) has been employed as a one‐step liquid‐free process combining polymerization and coating for the encapsulation of 3D non‐planar substrates. Coatings have been applied using iCVD specifically to encapsulate microparticles of a highly water‐soluble crop protection compound (CPC) for controlled release. Release behavior has been compared among different coatings synthesized using different iCVD processing conditions, including varying degrees of polymer hydrophobicity, continuous and pulsed deposition, and crosslinking. iCVD has been found to provide tunable synthesis of hydrophobic, crosslinked polymers with control over mass diffusivity, and coating thickness for enhancing barrier properties.
Tenofovir: Quo Vadis Anno 2012 (Where Is It Going in the Year 2012)?
Authors: De Clercq Erik
Published: May 2012

Twenty years after its original discovery, tenofovir has acquired a crucial position in the fight against human immunodeficiency virus (HIV). First, tenofovir disoproxil fumarate (TDF) is not only efficacious against, and has been licensed for the treatment of HIV (AIDS), but also HBV (hepatitis B). Second, for the treatment of HIV infections, TDF can be used in combination with other anti‐HIV drugs, such as emtricitabine (combination termed Truvada®) and Truvada can be further combined with efavirenz, rilpivirine, elvitegravir, atazanavir, or darunavir, as a single once‐daily oral pill. Third, Truvada can be used prophylactically to prevent transmission of HIV infection. And fourth, to prevent sexual HIV transmission, tenofovir could also be used topically (i.e., as a vaginal gel). © 2012 Wiley Periodicals, Inc. Med Res Rev., 32, No. 4, 765‐785, 2012
Reduction of the radiofrequency heating of metallic devices using a dual‐drive birdcage coil
Authors: Eryaman Yigitcan , Turk Esra Abaci , Oto Cagdas , Algin Oktay , Atalar Ergin
Published: May 2012

In this work, it is demonstrated that a dual‐drive birdcage coil can be used to reduce the radiofrequency heating of metallic devices during magnetic resonance imaging. By controlling the excitation currents of the two channels of a birdcage coil, the radiofrequency current that is induced near the lead tip could be set to zero. To monitor the current, the image artifacts near the lead tips were measured. The electric field distribution was controlled using a dual‐drive birdcage coil. With this method, the lead currents and the lead tip temperatures were reduced substantially [<0.3°C for an applied 4.4 W/kg SAR compared to >4.9°C using quadrature excitation], as demonstrated by phantom and animal experiments. The homogeneity of the flip angle distribution was preserved, as shown by volunteer experiments. The normalized root‐mean‐square error of the flip angle distribution was less than 10% for all excitations. The average specific absorption rate increased as a trade‐off for using different excitation patterns. Magn Reson Med, 2013. © 2012 Wiley Periodicals, Inc.
Irreversible change in the T1 temperature dependence with thermal dose using the proton resonance frequency‐T1 technique
Authors: Diakite Mahamadou , Payne Allison , Todd Nick , Parker Dennis L.
Published: May 2012

Denaturation of macromolecules within the tissues is believed to be the major factor contributing to the damage of tissues upon hyperthermia. As a result, the value of the spin‐lattice relaxation time T1 of the tissue water, which is related to the translational and rotational rates of water, represents an intrinsic probe for investigating structural changes in tissues at high temperature. Therefore, the goal of this work is to investigate whether the simultaneous measurement of temperature and T1 using a hybrid proton resonance frequency (PRF)‐T1 measurement technique can be used to detect irreversible changes in T1 that might be indicative of tissue damage. A new hybrid PRF‐T1 sequence was implemented based on the variable flip angle driven‐equilibrium single‐pulse observation (DESPOT)1 method from a standard three dimensional segmented echo‐planar imaging sequence by alternating two flip angles from measurement to measurement. The structural changes of the heated tissue volumes were analyzed based on the derived T1 values and the corresponding PRF temperatures. Using the hybrid PRF‐T1 technique, we demonstrate that the change of spin lattice relaxation time T1 is reversible with temperature for low thermal dose (thermal dose ≤ 240 cumulative equivalent minutes [CEM] 43°C) and irreversible with temperature after significant accumulation of thermal dose in ex vivo chicken breast tissue. These results suggest that the hybrid PRF‐T1 method may be a potentially powerful tool to investigate the extent and mechanism of heat damage of biological tissues. Magn Reson Med 69:1122–1130, 2013. © 2012 Wiley Periodicals, Inc.
Optimal magnetic susceptibility matching in 3D
Authors: Jia Feng , Kumar Rajesh , Korvink Jan G.
Published: May 2012

When an object is inserted into the strong homogeneous magnetic field of a magnetic resonance magnet, its intrinsic relative susceptibility can cause unwanted local magnetic field inhomogeneities in the space surrounding the object. As is known, this effect can be partially countered by selectively adding material layers with opposing sign in susceptibility to the part. The determination of an optimal magnetic susceptibility distribution is an inverse problem, in which the susceptibility‐induced inhomogeneity of the magnetic field inside a region of interest is reduced by redistributing the placement of materials in the design domain. This article proposes an efficient numerical topology optimization method for obtaining an optimal magnetic susceptibility distribution, in particular, for which the induced spatial magnetic field inhomogeneity is minimized. Using a material density function as a design variable, the value of the magnetic field inside a computational domain is determined using a finite element method. The first‐order sensitivity of the objective function is calculated using an adjoint equation method. Numerical examples on a variety of design domain geometries illustrate the effectiveness of the optimization method. The method is of specific interest for the design of interventional magnetic resonance devices. It is a particularly useful method if passive shimming of magnetic resonance equipment is aimed for. Magn Reson Med 69:1146–1156, 2013. © 2012 Wiley Periodicals, Inc.
Heterogeneous distribution of myocardial steatosis—An ex vivo evaluation
Authors: Liu Chia‐Ying , Liu Yuan Chang , Venkatesh Bharath Ambale , Lima Joao A. C. , Bluemke David A. , Steenbergen Charles
Published: May 2012

Myocardial fat accumulation could occur in diseased hearts. The degree of heterogeneity is unknown because accurate assessment is difficult using conventional proton magnetic resonance spectroscopy techniques in a beating heart. The purpose of this study was to characterize the distribution of intramyocellular lipid content and to determine its association with disease characteristics. Proton magnetic resonance spectroscopy was performed on formalin‐fixed slices of human hearts at various circumferential locations (N = 55). Twenty‐nine percent of the hearts had the highest fat content measured in the septum, followed by posterior (27%), lateral (26%), and anterior (18%) wall. Age was significantly correlated with the mean fat percentages (r2 = 0.12, P = 0.007). Those who died from cardiovascular disease demonstrated significantly higher and more heterogeneous fat distribution than those who did not (1.62% ± 1.1% vs. 0.59% ± 0.4%, P = 0.002). In summary, septal fat content is representative of mean fat percentage. Fat content increases with age; fat distribution may be heterogeneous when associated with cardiovascular disease. Magn Reson Med, 2012. © 2012 Wiley Periodicals, Inc.
Noninvasive prenatal detection of chromosomal aneuploidies using different next generation sequencing strategies and algorithms
Authors: Stumm Markus , Entezami Michael , Trunk Nastasja , Beck Martina , Löcherbach Julia , Wegner Rolf‐Dieter , Hagen Andreas , Becker Rolf , Hofmann Wera
Published: May 2012

Objective

Here we describe the successful application of massively parallel sequencing for noninvasive prenatal detection of trisomy 21. In addition, for the detection of a broader spectrum of fetal aneuploidies, a target enrichment approach was successfully tested.

Methods

The circulating cell‐free DNA was prepared from 53 maternal blood samples and analysed using Illumina's sequencing systems Genome AnalyzerIIx and HiSeq2000, respectively. In a first experiment the SureSelect Target Enrichment System was tested.

Results

In our initial study analysing 42 samples on the Genome AnalyzerIIx, all eight samples from women carrying a trisomy 21 fetus were correctly identified. On the basis of our HiSeq2000 sequence data, we discussed new algorithms for detection of fetal trisomy 21. In addition, we successfully used the combination of a target enrichment system followed by sequencing and were able to identify fetal trisomy 13 and fetal trisomy 21.

Conclusions

Our results confirm previous reports that massively parallel sequencing of cell‐free fetal DNA allows the reliably noninvasive detection of trisomy 21 from maternal blood with the potential to enhance test selectivity and specificity by bioinformatic means. According to our preliminary results, targeted sequencing might be an alternative strategy to detect chromosomal aneuploidies besides trisomy 21. © 2012 John Wiley & Sons, Ltd.
Synthesis of poly(ethylene terephthalate) in benzyl imidazolium ionic liquids
Authors: Dou Junyan , Liu Zhengping , Mahmood Khalid , Zhao Yuntao
Published: May 2012

In order to improve the method of synthesis of poly(ethylene terephthalate) (PET), a series of ionic liquids (ILs) based on benzyl imidazolium ([YBMIM][X], Y = NO2, CH3, F; B = benzyl; X = Tf2N) were used to investigate the formation of PET at low temperature and pressure. High molecular weight PET (Mw up to 2.6 × 104 g mol−1) was obtained by two‐step polycondensation in these ILs at lower temperature (230–240 °C) than with traditional melt polycondensation (270–290 °C). Moreover, the molecular weight of the resulting PET was found to depend on the activities of the catalysts used in the ILs. The catalysts (Sb2(OCH2CH2O)3, Sb(OAc)3, Sb2O3) used in the preparation of PET have little effect on the thermostability of the ILs. The ILs can decrease the viscosity of the reaction system, and thus small molecules can be easily removed. Copyright © 2012 Society of Chemical Industry
Investigation of polymerization of benzoxazines and thermal degradation characteristics of polybenzoxazines via direct pyrolysis mass spectrometry
Authors: Fam Shahla Bagheri , Uyar Tamer , Ishida Hatsuo , Hacaloglu Jale
Published: May 2012

Polymerization of benzoxazines and thermal degradation mechanisms of polybenzoxazines were investigated using the direct pyrolysis mass spectrometry (DP‐MS) technique. The benzoxazine structures were based on phenol and aniline and on bisphenol‐A and methylamine or aniline. Polymerizations of the benzoxazines were carried out by curing them at elevated temperatures without addition of initiator or catalyst. DP‐MS data showed the presence of chains generated by opposing polymerization reaction pathways indicating quite complex structures for the polybenzoxazines under investigation. Thermal decomposition of polybenzoxazines was started by the cleavage of methylamine or aniline linkages. It was determined that polybenzoxazines based on phenol were more stable than the corresponding bisphenol‐A‐based polybenzoxazines, while those based on methylamine were more stable than the corresponding polybenzoxazines incorporating aniline. Thus, it can be concluded that the presence of bulky groups decreased the extent of crosslinking which in return decreased the thermal stability. Copyright © 2012 Society of Chemical Industry
Information‐dependent LC‐MS/MS acquisition with exclusion lists potentially generated on‐the‐fly: Case study using a whole cell digest of Clostridium thermocellum
Authors: McQueen Peter , Spicer Vic , Rydzak Thomas , Sparling Richard , Levin David , Wilkins John A. , Krokhin Oleg
Published: May 2012

We have developed a real‐time graphic‐processor‐unit‐based search engine capable of high‐quality peptide identifications in <500 μs per spectrum. The steps of peptide/protein identification, in‐silico prediction of all possible tryptic peptides from these proteins, and the prediction of their expected retention times and m/z values take less than 5 s per cycle over ∼3000 MS/MS spectra. This lays the foundation for information‐dependent acquisition with exclusion lists generated on‐the‐fly, as the instrument continues to acquire data. While a complete evaluation of the dynamic exclusion system requires the participation from instrument vendors, we conducted a series of model experiments using a whole cell tryptic digestion of the bacterium Clostridium thermocellum. We ran a series of five iterative LC‐MS/MS runs, adding a new exclusion list at each of four chromatographic “tripping points” – the elution times of the four standard peptides spiked into the sample. Retention times of these standard peptides were also used for real‐time “chromatographic calibration.” The dynamic exclusion approach gave a ∼5% increase in confident protein identification (for typical 2 h LC‐MS/MS run), and reduced the average number of identified peptides per protein from 4.7 to 2.9. Its application to a two‐times shorter gradient gave a ∼17% increase in proteins identified. Further improvements are possible for instruments with better mass accuracy, by employing a more accurate retention prediction algorithm and by developing better understanding of the possible chemical modifications and fragmentations produced during electrospray ionization.
Application of targeted proteomics to metabolically engineered Escherichia coli
Authors: Singh Pragya , Batth Tanveer S. , Juminaga Darmawi , Dahl Robert H. , Keasling Jay D. , Adams Paul D. , Petzold Christopher J.
Published: May 2012

As synthetic biology matures to compete with chemical transformation of commodity and high‐value compounds, a wide variety of well‐characterized biological parts are needed to facilitate system design. Protein quantification based on selected‐reaction monitoring (SRM) mass spectrometry compliments metabolite and transcript analysis for system characterization and optimizing flux through engineered pathways. By using SRM quantification, we assayed red fluorescent protein (RFP) expressed from plasmids containing several inducible and constitutive promoters and subsequently assessed protein production from the same promoters driving expression of eight mevalonate pathway proteins in Escherichia coli. For each of the promoter systems, the protein level for the first gene in the operon followed that of RFP, however, the levels of proteins produced from genes farther from the promoter were much less consistent. Second, we used targeted proteomics to characterize tyrosine biosynthesis pathway proteins after removal of native regulation. The changes were not expected to cause significant impact on protein levels, yet significant variation in protein abundance was observed and tyrosine production for these strains spanned a range from less than 1 mg/L to greater than 250 mg/L. Overall, our results underscore the importance of targeted proteomics for determining accurate protein levels in engineered systems and fine‐tuning metabolic pathways.
Highly multiplexed targeted proteomics using precise control of peptide retention time
Authors: Gallien Sebastien , Peterman Scott , Kiyonami Reiko , Souady Jamal , Duriez Elodie , Schoen Alan , Domon Bruno
Published: May 2012

Large‐scale proteomics applications using SRM analysis on triple quadrupole mass spectrometers present new challenges to LC‐MS/MS experimental design. Despite the automation of building large‐scale LC‐SRM methods, the increased numbers of targeted peptides can compromise the balance between sensitivity and selectivity. To facilitate large target numbers, time‐scheduled SRM transition acquisition is performed. Previously published results have demonstrated incorporation of a well‐characterized set of synthetic peptides enabled chromatographic characterization of the elution profile for most endogenous peptides. We have extended this application of peptide trainer kits to not only build SRM methods but to facilitate real‐time elution profile characterization that enables automated adjustment of the scheduled detection windows. Incorporation of dynamic retention time adjustments better facilitate targeted assays lasting several days without the need for constant supervision. This paper provides an overview of how the dynamic retention correction approach identifies and corrects for commonly observed LC variations. This adjustment dramatically improves robustness in targeted discovery experiments as well as routine quantification experiments.
Range of protein detection by selected/multiple reaction monitoring mass spectrometry in an unfractionated human cell culture lysate
Authors: Ebhardt H. Alexander , Sabidó Eduard , Hüttenhain Ruth , Collins Ben , Aebersold Ruedi
Published: May 2012

Selected or multiple reaction monitoring is a targeted mass spectrometry method (S/MRM‐MS), in which many peptides are simultaneously and consistently analyzed during a single liquid chromatography‐mass spectrometry (LC‐S/MRM‐MS) measurement. These capabilities make S/MRM‐MS an attractive method to monitor a consistent set of proteins over various experimental conditions. To increase throughput for S/MRM‐MS it is advantageous to use scheduled methods and unfractionated protein extracts. Here, we established the practically measurable dynamic range of proteins reliably detectable and quantifiable in an unfractionated protein extract from a human cell line using LC‐S/MRM‐MS. Initially, we analyzed S/MRM transition peak groups in terms of interfering signals and compared S/MRM transition peak groups to MS1‐triggered MS2 spectra using dot‐product analysis. Finally, using unfractionated protein extract from human cell lysate, we quantified the upper boundary of copies per cell to be 35 million copies per cell, while 7500 copies per cell represents a lower boundary using a single 35 min linear gradient LC‐S/MRM‐MS measurement on a current, standard commercial instrument.