bluuebunny/crossref_metadata_2025 huggingface dataset:
Using Huffman coding method to visualize and analyze DNA sequences
Authors: Qi Zhao‐Hui , Li Ling , Qi Xiao‐Qin
Published: September 2011

On the basis of the Huffman coding method, we propose a new graphical representation of DNA sequence. The representation can avoid degeneracy and loss of information in the transfer of data from a DNA sequence to its graphical representation. Then a multicomponent vector from the representation is introduced to characterize quantitatively DNA sequences. The components of the vector are derived from the graphical representation of DNA primary sequence. The examination of similarities and dissimilarities among the complete coding sequences of β‐globin gene of 11 species and six ND6 proteins shows the utility of the scheme. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Molecular dynamics simulations of triflic acid and triflate ion/water mixtures: A proton conducting electrolytic component in fuel cells
Authors: Sunda Anurag Prakash , Venkatnathan Arun
Published: September 2011

Triflic acid is a functional group of perflourosulfonated polymer electrolyte membranes where the sulfonate group is responsible for proton conduction. However, even at extremely low hydration, triflic acid exists as a triflate ion. In this work, we have developed a force‐field for triflic acid and triflate ion by deriving force‐field parameters using ab initio calculations and incorporated these parameters with the Optimized Potentials for Liquid Simulations ‐ All Atom (OPLS‐AA) force‐field. We have employed classical molecular dynamics (MD) simulations with the developed force field to characterize structural and dynamical properties of triflic acid (270–450 K) and triflate ion/water mixtures (300 K). The radial distribution functions (RDFs) show the hydrophobic nature of CF3 group and presence of strong hydrogen bonding in triflic acid and temperature has an insignificant effect. Results from our MD simulations show that the diffusion of triflic acid increases with temperature. The RDFs from triflate ion/water mixtures shows that increasing hydration causes water molecules to orient around the SO3− group of triflate ions, solvate the hydronium ions, and other water molecules. The diffusion of triflate ions, hydronium ion, and water molecules shows an increase with hydration. At λ = 1, the diffusion of triflate ion is 30 times lower than the diffusion of triflic acid due to the formation of stable triflate ion–hydronium ion complex. With increasing hydration, water molecules break the stability of triflate ion–hydronium ion complex leading to enhanced diffusion. The RDFs and diffusion coefficients of triflate ions, hydronium ions and water molecules resemble qualitatively the previous findings using per‐fluorosulfonated membranes. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Optimal (v, 4, 2, 1) optical orthogonal codes with small parameters
Authors: Baicheva Tsonka , Topalova Svetlana
Published: September 2011

Optimal (v, 4,2,1) optical orthogonal codes (OOCs) with v⩽75 and v≠71 are classified up to isomorphism. One (v, 4,2,1) OOC is presented for all v⩽181, for which an optimal OOC exists. Copyright © 2011 Wiley Periodicals, Inc. J Combin Designs 20:142‐160, 2012
Trivalent chromium removal from tannery effluent using kaolin‐supported bacterial biofilm of Bacillus sp isolated from chromium polluted soil
Authors: Fathima Aafreen , Rao Jonnalagadda Raghava , Unni Nair Balachandran
Published: September 2011

BACKGROUND: Bacterial strains belonging to the genus Bacillus, isolated from Cr‐ polluted soil (tannery sludge) were employed as consortium for Cr(III) removal from tannery effluents. Kaolin clay, a natural adsorbent, was used as supporting material for bacterial biofilm formation. The use of clay‐supported bacterial biofilm has not previously been employed for the treatment of tannery effluents containing Cr(III) salt.

RESULTS: Commercial tannery effluent containing 1000 ppm initial metal ion concentration was treated in stages. The initial Cr(III) concentration of 1000 ppm was brought down to 2 ppm, a permissible level for discharge, after the fourth stage. The bacterial isolates were found to be Bacillus subtilis VITSCCr01 and Bacillus cereus VITSCCr02 by 16s rRNA gene sequencing. Batch assay and confocal laser scanning microscopy results revealed the role of kaolin as a support material in biofilm formation. Best fit was obtained with the Freundlich adsorption isotherm. The mechanism of sorption was confirmed by Fourier transform infrared (FT‐IR) spectroscopy and scanning electron microscopy–energy dispersive X‐ray spectroscopy (SEM‐EDS).

CONCLUSION: Cr(III) removal from tannery effluent using low cost adsorbents such as kaolin and bacteria proved to be effective for metal concentrations ⩽1000 ppm; this is normally not possible using conventional treatment methods. This work has demonstrated feasible sorption of Cr(III), especially during post‐tanning operations. Copyright © 2011 Society of Chemical Industry
Context matters: Combined influence of participation and intellectual stimulation on the promotion focus–employee creativity relationship
Authors: Zhou Qin , Hirst Giles , Shipton Helen
Published: September 2011

In this paper, we examined the interactive effects of two contexts—participation and intellectual stimulation, and promotion focus on creativity. On the basis of a multi‐organization sample of 213 employees, we tested and found that although promotion focus was positively related to creativity, the relationship between promotion focus and creativity was most positive when both participation and leader intellectual stimulation were high. We discuss the way contexts in combination influence employee creativity for promotion‐oriented individuals, through increasing decision latitude as well as stimulating and promoting creativity. Copyright © 2011 John Wiley & Sons, Ltd.
Antioxidants from barley husks impregnated in films of low‐density polyethylene and their effect over lipid deterioration of frozen cod (Gadus morhua)
Authors: Pereira de Abreu David A , Maroto Julio , Villalba Rodríguez Karen , Cruz José M
Published: September 2011

BACKGROUND: The changes in quality of cod fillets packaged in films with and without antioxidants during 12 months of frozen storage at − 20 °C were investigated in the present study. The following parameters were determined in order to study lipid hydrolysis and primary and secondary lipid oxidation in the samples during frozen storage: peroxide value, conjugated dienes, conjugated triene hydroperoxides, free fatty acids, totox value, thiobarbituric acid‐reactive substances and p‐anisidine value.

RESULTS: Films containing antioxidants isolated from barley husks were effective in slowing down lipid hydrolysis and primary and secondary lipid oxidation processes. Secondary lipid oxidation reached maximum values in the 12th month of storage in control samples and samples packaged with antioxidant‐containing film. Maximum lipid hydrolysis and lipid oxidation values for control cod samples were significantly higher than the maximum values found in samples packaged with antioxidant‐containing film.

CONCLUSION: The results confirm the efficacy of natural antioxidants derived from barley husks in slowing down lipid hydrolysis and increasing the oxidative stability of cod flesh. They also demonstrate the potential usefulness of natural antioxidants extracted from barley husks in the development of active packaging films for food preservation. Copyright © 2011 Society of Chemical Industry
Evaluation of processed green and ripe mango peel and pulp flours (Mangifera indica var. Chokanan) in terms of chemical composition, antioxidant compounds and functional properties
Authors: Abdul Aziz Noor Aziah , Wong Lee Min , Bhat Rajeev , Cheng Lai Hoong
Published: September 2011

BACKGROUND: Mango is a highly perishable seasonal fruit and large quantities are wasted during the peak season as a result of poor postharvest handling procedures. Processing surplus mango fruits into flour to be used as a functional ingredient appears to be a good preservation method to ensure its extended consumption.

RESULTS: In the present study, the chemical composition, bioactive/antioxidant compounds and functional properties of green and ripe mango (Mangifera indica var. Chokanan) peel and pulp flours were evaluated. Compared to commercial wheat flour, mango flours were significantly low in moisture and protein, but were high in crude fiber, fat and ash content. Mango flour showed a balance between soluble and insoluble dietary fiber proportions, with total dietary fiber content ranging from 3.2 to 5.94 g kg−1. Mango flours exhibited high values for bioactive/antioxidant compounds compared to wheat flour. The water absorption capacity and oil absorption capacity of mango flours ranged from 0.36 to 0.87 g kg−1 and from 0.18 to 0.22 g kg−1, respectively.

CONCLUSION: Results of this study showed mango peel flour to be a rich source of dietary fiber with good antioxidant and functional properties, which could be a useful ingredient for new functional food formulations. Copyright © 2011 Society of Chemical Industry
Use of plant residues on growth of mycorrhizal seedlings of neem (Azadirachta indica A. Juss.)
Authors: Monte Júnior Inácio P , Maia Leonor C , Silva Fábio SB , Cavalcante Uided MT
Published: September 2011

BACKGROUND: Owing to its multiple uses in veterinary medicine, biofertilizers, pest control, etc., the commercial cultivation of neem (Azadirachta indica) has been increasing in various countries. The use of arbuscular mycorrhizal fungi (AMF) and plant by‐products (composted leaves and residues of neem and sugarcane) for the propagation of seedlings can be an efficient alternative to stimulate plant growth, reducing the propagation time and conferring increased tolerance of plants to biotic and abiotic stresses. Therefore this study aimed to evaluate the effect of plant substrates and inoculation with AMF on the production of neem seedlings.

RESULTS: Beneficial effects of the application of neem by‐products to neem seedlings were observed on most of the variables analysed. However, the treatment with sugarcane cake did not improve the growth of neem seedlings. In general, the inoculation treatments using Glomus etunicatum in the composted neem substrates improved seedling growth.

CONCLUSION: Neem by‐products benefit the growth of seedlings of this plant under greenhouse conditions. Inoculation with G. etunicatum enhances plants growth mainly in substrates with residues of neem leaves, providing an alternative for the production of seedlings of this crop under nursery conditions, which can reduce the need for chemical fertilizers that impact the environment. Copyright © 2011 Society of Chemical Industry
Down‐regulated SPARCL1 is associated with clinical significance in human gastric cancer
Authors: Li Ping , Qian Jianxin , Yu Guanzhen , Chen Ying , Liu Ke , Li Jie , Wang Jiejun
Published: September 2011

Backgroud

SPARC‐like protein 1 (SPARCL1), a member of extracelluar matrix glycoprotein, is involved in many physiological functions.

Methods

Tissue microarray (TMA) blocks were constructed based on 1,072 Chinese patients, containing both gastric cancer (GC) tissues and adjacent normal mucosa tissues. We analyzed the expression of SPARCL1 from both mRNA and protein level, using Real‐time quantitative polymerase chain reaction (qRT‐PCR), semi‐quantitative PCR, immunohistochemistry (IHC), and Western blotting. Loss of heterozygosity analysis at the SPARCL1 gene locus was carried out using ten paired tumor and matched normal tissues.

Results

SPARCL1 mRNA was significantly reduced in tumor specimens compared with normal tissues. Down‐regulation of SPARCL1 protein was detected in 413 cases (38.7%) of 1,072 primary gastric tumor tissues. Kaplan–Meier survival curves demonstrated that SPARCL1‐positive patients had better median survival time than SPARCL1‐negative patients (59 months vs. 28 months, P = 0.001). Multivariate survival analysis revealed that SPARCL1 was an independent prognostic factor in gastric adenocarcinoma patients with no metastasis and well/moderately differentiated. The incidence of LOH for each individual marker was 12.5% (1/8) for D4S2462, 20% (2/10) for D4S2929, and 33.3% (3/9) for SPARCL1.

Conclusions

Our study revealed the clinical significance of SPARCL1 expression, providing a basis that the loss of SPARCL1 is a negative event in GC progression and prognosis. Furthermore, SPARCL1 protein might be considered to be a potential differentiation marker. J. Surg. Oncol. 2012; 105:31–37. © 2011 Wiley Periodicals, Inc.
New hierarchically porous titania monoliths for chromatographic separation media
Authors: Hasegawa George , Morisato Kei , Kanamori Kazuyoshi , Nakanishi Kazuki
Published: September 2011

Separation media based on hierarchically porous titania (TiO2) monoliths for high‐performance liquid chromatography (HPLC) have been successfully fabricated by the sol–gel process of titanium alkoxide in a mild condition utilizing a chelating agent and mineral salt. The as‐gelled TiO2 monoliths were subjected to a simple solvent exchange process from ethanol (EtOH) to H2O followed by drying and calcination. The resultant monolithic TiO2 columns consist of anatase crystallites with the typical specific surface area of more than 200 m2/g. The resultant monolithic TiO2 column calcined at 200 and 400°C exhibited a good separation performance for organophosphates as well as for polar benzene derivatives in the normal‐phase mode.
PTSD and alcohol use after the World Trade Center attacks: A longitudinal study
Authors: Boscarino Joseph A. , Kirchner H. Lester , Hoffman Stuart N. , Sartorius Jennifer , Adams Richard E.
Published: September 2011

Research suggests that posttraumatic stress disorder (PTSD) is associated with increased alcohol use, but the findings have not been consistent. We assessed alcohol use, binge drinking, and psychotropic medication use longitudinally in 1,681 New York City adults, representative of the 2000 census, 2 years after the World Trade Center attacks. We found that, with the exception of a modified CAGE Questionnaire index for alcohol, alcohol use showed a modest increase over time and was related to PTSD symptoms, with an increase of about 1 more drink per month for those with PTSD, even though overall levels appeared to be within the National Institute on Alcohol Abuse and Alcoholism's safe range. Psychotropic medication use followed a similar trend; those with PTSD used psychotropics about 20 more days over the past year than those without. Because the study analyses adjusted for key psychosocial variables and confounders, it is not clear if the increased alcohol use following trauma exposure is associated with self‐medication of PTSD symptoms, whether increased alcohol use prior to exposure is a risk for delayed‐onset PTSD, or whether a third unmeasured variable is involved. Further research is warranted.
Cognitive and emotional contributors to intimate partner violence perpetration following trauma
Authors: Marshall Amy D. , Robinson Lara R. , Azar Sandra T.
Published: September 2011

Exposure to potentially traumatic events often leads to a wide range of interpersonal difficulties, including the perpetration of intimate partner violence. Maladaptive, threat‐relevant thoughts and beliefs regarding the trauma or its sequelae can play an important role in a person's emotional and behavioral responses. Among 185 trauma‐exposed study participants who were currently in an intimate relationship, levels of maladaptive posttraumatic cognitions were associated with the perpetration of psychological aggression and physical violence in their current relationships. These links were mediated by misappraisal of anger in auditory emotion stimuli and emotion‐regulation deficits. Results support a cognitive model of posttraumatic pathology, with implications for clinical intervention and a broad conceptualization of the effects of trauma.
Reactions to trauma research among women recently exposed to a campus shooting
Authors: Fergus Thomas A. , Rabenhorst Mandy M. , Orcutt Holly K. , Valentiner David P.
Published: September 2011

Subjective and objective reactions to writing and reading a narrative of their experiences after having been recently exposed to a campus shooting were examined in 58 women. Posttraumatic stress, depression, anxiety symptoms, and physical exposure to the shooting were considered in relation to laboratory indices. The latter used a multimethod approach to index distress; these included subjective (self‐report) and objective (heart rate, skin conductance, and cortisol) components. Consistent with prior research, reports of symptoms were significantly positively correlated with subjective distress (r ranged from .35 to .45), but only posttraumatic stress symptoms uniquely predicted subjective distress in regression analyses (partial r = .33). Objective distress, however, was not significantly related to any participant measure. Finally, a clear majority (85%) of participants reported they would participate in the study again. Points of convergence and divergence with prior studies are discussed.
New Alternating Copolymers of 3,6‐Carbazoles and Dithienylbenzothiadiazoles: Synthesis, Characterization, and Application in Photovoltaics
Authors: Berton Nicolas , Ottone Chiara , Labet Vanessa , de Bettignies Rémi , Bailly Séverine , Grand André , Morell Christophe , Sadki Saïd , Chandezon Frédéric
Published: September 2011

Three new low‐bandgap copolymers containing 3,6‐linked carbazole units are synthesized and characterized using a combination of spectroscopic and electrochemical techniques and DFT calculations. The electron‐withdrawing effect of the BTD units leads to a significant decrease of the optical bandgap from 2.59 eV for PBTC to 1.81 eV for PCDTBT, whereas pendant octyl chains on the thiophene ring lead to an increase of the gap to 2.05 eV for PCDOTBT due to steric hindrance. PBTC:PCBM photovoltaic devices exhibit a PCE of 0.35% with an EQE reaching 35% in the blue region of the solar spectrum whereas PCDTBT:PCBM blends are efficient over a wider spectral range due to the lower bandgap of PCDTBT.

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Low‐Stress Hyperbranched Polymer/Silica Nanostructures Produced by UV Curing, Sol/Gel Processing and Nanoimprint Lithography
Authors: Geiser Valérie , Leterrier Yves , Månson Jan‐Anders E.
Published: September 2011

Nanocomposite materials based on a HBP and silica are produced using either a dual‐cure sol/gel and photopolymerization process or by mixing silica nanoparticles with the HBP. In both cases the conversion of the HBP is independent of composition and obeys a time‐intensity superposition with power‐law dependence on UV intensity. Optimization of the dual‐cure process leads to transparent sol/gel composites with ultrafine structures. These materials systematically outperform the particulate composites, including an increase of the glass transition temperature of 63 °C and a process‐induced internal stress as low as 2.5 MPa. Nano‐sized gratings are produced from the sol/gel composites by low‐pressure UV nanoimprint lithography.

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Characterization of a Silk‐Resinified Compact Fabricated Using a Pulse‐Energizing Sintering Device
Authors: Kaneko Atsushi , Tamada Yasushi , Hirai Shinji , Kuzuya Toshihiro , Hashimoto Tomoko
Published: September 2011

Pulse electric current sintering is used to prepare a compact from resinificated hydrous silk powder. Compacts with no remnant silk powders are formed with 20 wt% added water, 20–40 MPa molding pressure, and >353 K molding temperature. The latter two are much lower than those used for conventional hot pressing. No dependence on molding pressure and temperature are found in XRD or FT‐IR analysis, except for a compact molded at 473 K, for which silk fibroin decomposition is confirmed by DSC, EGA‐MS, and molecular weight measurements. The compact's three‐point bending strength depends on the molding temperature, except for the temperature at which silk fibroin decomposes. The maximum three‐point bending strength resembles that of general‐purpose epoxy resin and is much higher than that of PLA.

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Polyester Preparation in the Presence of Pristine and Phosphonic‐Acid‐Modified Zirconia Nanopowders
Authors: Svehla Jakob , Pabisch Silvia , Feichtenschlager Bernhard , Holzmann Dietmar , Peterlik Herwig , Kickelbick Guido
Published: September 2011

A novel zirconia polyester nanocomposite is prepared using an in situ approach. Surface‐functionalized zirconia nanoparticles are obtained by attaching 3‐phosphonopropionic acid to the metal oxide. Neat and surface‐covered metal oxide particles are incorporated at the beginning of the polyesterification reaction of isophthalic acid and neopentyl glycol resulting in zirconia/poly(neopentyl isophthalate) (PNI) nanocomposites. TEM shows that the dispersibility of the inorganic filler is improved by covering the zirconia surface with carboxylic acid groups. These results are verified by SAXS. Rheological measurements reveal that the viscosities are increasing compared to pristine PNI at particle loads of 10 wt% (neat zirconia) and 5 wt% (phosphonic‐acid‐capped zirconia), respectively.

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Unveiling videos: Consumer‐generated ads as qualitative inquiry
Authors: Berthon Pierre , Pitt Leyland , DesAutels Philip
Published: September 2011

Companies spend millions of dollars researching consumers, consumer attitudes to brands, and consumer uses of products. Yet the irony is that consumers are now doing this research themselves and posting their material to video‐sharing sites such as YouTube. In this paper we argue that the BASIC IDS framework (Cohen, 1999) for dimensional qualitative research can be used to deconstruct consumer‐generated videos to yield valuable insights into the paradoxes of consumer–service interactions. One category of service that has gained huge media attention of late, and yet is poorly understood, is the phenomenon of online social networks. Using three consumer‐generated ads about the social networking site Facebook, we explore the paradoxes of consumer–service interaction, namely consumers' ambivalent attitudes to the service, how the consumer uses and is used by the service, how the service both facilitates behavior and changes behavior, and how the service mediates social interactions yet drives social actors. Finally, we locate the findings in terms of the wider context of Gen Y and the digital revolution, specify limitations, and cite implications and avenues for future research. © 2011 Wiley Periodicals, Inc.
Synthesis of a Novel Fused Thiophene‐thieno[3,2‐b]thiophene‐thiophene Donor Monomer and Co‐polymer for Use in OPV and OFETs
Authors: Bronstein Hugo , Ashraf Raja Shahid , Kim Youngju , White Andrew J. P. , Anthopoulos Thomas , Song Kigook , James David , Zhang Weimin , McCulloch Iain
Published: September 2011

The synthesis of a novel fused hexacyclic electron rich monomer incorporating thieno[3,2‐b]thiophene is reported and characterized by single crystal X‐ray diffraction. Suzuki co‐polymerization with benzothiadiazole (BT) afforded a novel low band‐gap polymer P4TBT with high molecular weights and good solution processability. Bulk heterojunction solar cell devices using the P4TBT and [70]PCBM gave power conversion efficiencies of 2.5%. Top‐gate, bottom‐contact field effect transistors (FETs) using P4TBT displayed high hole mobilities of 0.07 cm2 · Vs−1 demonstrating the suitability of the novel monomer and polymer for use in high performing organic electronic devices.

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Branched Semiflexible Polymers: Theoretical and Simulation Aspects
Authors: Dolgushev Maxim , Berezovska Ganna , Blumen Alexander
Published: September 2011

Recent approaches for taking stiffness effects into account when modeling multifunctional polymer structures are reported. The theoretical part is focused on arbitrary tree‐like polymers, modeled through extensions of the GGS scheme that allows the inclusion of local constraints. The theoretical findings are compared to the results of numerical simulations in which stiffness is included into the bond fluctuation model with the help of additional bending potentials. The procedure is illustrated by evaluating the static properties of semiflexible linear chains, stars, cospectral polymers and rings. The dynamical properties are exemplified by the mechanical relaxation of semiflexible polymers, including situations in which the local conditions at different sites are the same or different.

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Green tea catechin extract in intervention of chronic breast cell carcinogenesis induced by environmental carcinogens
Authors: Rathore Kusum , Wang Hwa‐Chain Robert
Published: September 2011

Sporadic breast cancers are mainly attributable to long‐term exposure to environmental factors, via a multi‐year, multi‐step, and multi‐path process of tumorigenesis involving cumulative genetic and epigenetic alterations in the chronic carcinogenesis of breast cells from a non‐cancerous stage to precancerous and cancerous stages. Epidemiologic and experimental studies have suggested that green tea components may be used as preventive agents for breast cancer control. In our research, we have developed a cellular model that mimics breast cell carcinogenesis chronically induced by cumulative exposures to low doses of environmental carcinogens. In this study, we used our chronic carcinogenesis model as a target system to investigate the activity of green tea catechin extract (GTC) at non‐cytotoxic levels in intervention of cellular carcinogenesis induced by cumulative exposures to pico‐molar 4‐(methylnitrosamino)‐1‐(3‐pyridyl)‐1‐butanone (NNK) and benzo[a]pyrene (B[a]P). We identified that GTC, at a non‐cytotoxic, physiologically achievable concentration of 2.5 µg/mL, was effective in suppressing NNK‐ and B[a]P‐induced cellular carcinogenesis, as measured by reduction of the acquired cancer‐associated properties of reduced dependence on growth factors, anchorage‐independent growth, increased cell mobility, and acinar‐conformational disruption. We also detected that intervention of carcinogen‐induced elevation of reactive oxygen species (ROS), increase of cell proliferation, activation of the ERK pathway, DNA damage, and changes in gene expression may account for the mechanisms of GTC's preventive activity. Thus, GTC may be used in dietary and chemoprevention of breast cell carcinogenesis associated with long‐term exposure to low doses of environmental carcinogens. © 2011 Wiley Periodicals, Inc.
SMAD4‐dependent polysome RNA recruitment in human pancreatic cancer cells
Authors: Thornley Jessica A. , Trask Heidi W. , Ringelberg Carol S. , Ridley Christian J.A. , Wang Sinny , Sal‐Lari Richard Cowper , Moore Jason H. , Korc Murray , Tomlinson Craig R.
Published: September 2011

Pancreatic cancer is the fourth leading cause of cancer death in the United States because most patients are diagnosed too late in the course of the disease to be treated effectively. Thus, there is a pressing need to more clearly understand how gene expression is regulated in cancer cells and to identify new biomarkers and therapeutic targets. Translational regulation is thought to occur primarily through non‐SMAD directed signaling pathways. We tested the hypothesis that SMAD4‐dependent signaling does play a role in the regulation of mRNA entry into polysomes and that novel candidate genes in pancreatic cancer could be identified using polysome RNA from the human pancreatic cancer cell line BxPC3 with or without a functional SMAD4 gene. We found that (i) differentially expressed whole cell and cytoplasm RNA levels are both poor predictors of polysome RNA levels; (ii) for a majority of RNAs, differential RNA levels are regulated independently in the nucleus, cytoplasm, and polysomes; (iii) for most of the remaining polysome RNA, levels are regulated via a “tagging” of the RNAs in the nucleus for rapid entry into the polysomes; (iv) a SMAD4‐dependent pathway appears to indeed play a role in regulating mRNA entry into polysomes; and (v) a gene list derived from differentially expressed polysome RNA in BxPC3 cells generated new candidate genes and cell pathways potentially related to pancreatic cancer. © 2011 Wiley Periodicals, Inc.
PAX3‐FOXO1 and FGFR4 in alveolar rhabdomyosarcoma
Authors: Marshall Amy D. , van der Ent Martijn A. , Grosveld Gerard C.
Published: September 2011

We and others have identified FGFR4 as a direct transcriptional target of the alveolar rhabdomyosarcoma (ARMS) specific fusion protein, PAX3‐FOXO1. We hypothesized fibroblast growth factor receptor 4 (FGFR4) may act as an effector of PAX3‐FOXO1, contributing to PAX3‐FOXO1 tumorigenic phenotypes. However, we demonstrate that enhanced expression of FGFR4 does not contribute to inhibited differentiation, enhanced proliferation, or transformation downstream of PAX3‐FOXO1 in primary mouse myoblasts. Therefore we were unable to identify any contribution of up regulation of wild type FGFR4 to PAX3‐FOXO1 driven tumorigenesis. Conversely, a constitutively active mutant of FGFR4 can enhance primary myoblast proliferation and transformation, indicating activating mutations of FGFR4 could contribute to the development and progression of ARMS. We sequenced the FGFR4 mRNA from five ARMS cell lines and identified no somatic mutations, nor any association with any human single nucleotide polymorphism within the FGFR4 coding region. © 2011 Wiley Periodicals, Inc.
Ras inhibition in hepatocarcinoma by S‐trans‐trans‐farnesylthiosalicyclic acid: Association of its tumor preventive effect with cell proliferation, cell cycle events, and angiogenesis
Authors: Stärkel Peter , Charette Nicolas , Borbath Ivan , Schneider‐Merck Tanja , De Saeger Christine , Abarca Jorge , Leclercq Isabelle , Horsmans Yves
Published: September 2011

Activation of Ras and its downstream signaling pathways, likely contribute to the development of hepatocarcinoma. We have previously shown that intraperitoneal injections of the Ras inhibitor S‐trans, trans‐farnesylthiosalicyclic acid (FTS) blocks Ras activation and prevents heptocarcinoma development in rats receiving weekly injections of the carcinogene diethylnitrosamine (DEN) for 16 wk. Using this in vivo model, we evaluated the relationship between the tumor preventive effect of Ras inhibition and activation of downstream signaling pathways, cell proliferation, cell cycle events, and angiogenesis. Western blotting, quantitative PCR, immunohistochemistry, and transcription factor activity assays were used. DEN‐induced activation of NFkB and Stat3 was abrogated by FTS treatment. FTS treatment showed no effect on DEN‐induced elevation of TNFα, interleukin 6 and TLR4, known activators of these transcription factors. FTS significantly reduced phosphorylation of the MAPkinase p38 and of the p70S6 kinase, a surrogate marker for mTor activation, without affecting ERK and AKT phosphorylation. These events were associated with reduced c‐myc and cyclin D expression as well as reduced cell proliferation in transformed, GSTp‐positive hepatocytes. Moreover, FTS treatment shifted cell proliferation from transformed hepatocytes to apparently normal, GSTp negative hepatocytes. FTS treatment did not down‐regulate expression of angiogenesis markers HIFα, VEGF, VEGF receptor1, and placenta growth factor. FTS treatment inhibits important signaling pathways involved in cellular proliferation leading to strongly reduced proliferation of transformed hepatocytes without affecting normal hepatocytes. This re‐adjustment of the proliferation balance likely contributes to the tumor preventive of FTS in the context of Ras inhibition in hepatocarcinogenesis. © 2011 Wiley Periodicals, Inc.
Allergenic and immunogenic potential of cow's milk β‐lactoglobulin and caseins evidenced without adjuvant in germ‐free mice
Authors: Morin Stéphanie , Bernard Hervé , Przybylski‐Nicaise Laetitia , Corthier Gérard , Rabot Sylvie , Wal Jean‐Michel , Hazebrouck Stéphane
Published: September 2011

Scope: In most animal models of allergy, the development of an IgE response requires the use of an adjuvant. Germ‐free (GF) mice exhibit Th2‐polarized antibody responses combined with defective immunosuppressive mechanisms. The sensitizing potential of milk proteins was investigated in GF mice in the absence of adjuvant.

Methods and results: β‐lactoglobulin (BLG) and whole casein (CAS) allergenicity was evaluated by means of intraperitoneal injections without adjuvant. Injections of BLG induced significant IgE and IgG1 responses in GF mice, while CAS injections provoked the production of IgG1 toward κ‐ and αS1‐caseins. No significant antibody response was evidenced in conventional (CV) mice. After in vitro BLG‐reactivation, IL‐4, IL‐5, IL‐13 and IFN‐γ productions by splenocytes were higher in GF mice than in CV mice. Heat‐treatment decreased BLG allergenicity as indicated by the absence of IgE production in GF mice. However, heat‐treatment increased protein immunogenicity and led to the production of anti‐BLG and anti‐κ‐casein IgG1 in both GF and CV mice. This correlated with enhanced productions of IL‐4, IL‐5 and IL‐13 in BLG‐reactivated splenocytes from CV mice.

Conclusion: Gut colonization by commensal bacteria appeared then to significantly reduce the susceptibility of mice toward the intrinsic allergenic and immunogenic potential of milk proteins.
Ginger phytochemicals mitigate the obesogenic effects of a high‐fat diet in mice: A proteomic and biomarker network analysis
Authors: Beattie John H. , Nicol Fergus , Gordon Margaret‐Jane , Reid Martin D. , Cantlay Louise , Horgan Graham W. , Kwun In‐Sook , Ahn Ji‐Yun , Ha Tae‐Youl
Published: September 2011

Scope: Natural dietary anti‐obesogenic phytochemicals may help combat the rising global incidence of obesity. We aimed to identify key hepatic pathways targeted by anti‐obsogenic ginger phytochemicals fed to mice.

Methods and results: Weaning mice were fed a high‐fat diet containing 6‐gingerol (HFG), zerumbone (HFZ), a characterized rhizome extract of the ginger‐related plant Alpinia officinarum Hance (high fat goryankang, HFGK) or no phytochemicals (high‐fat control, HFC) for 6 wks and were compared with mice on a low‐fat control diet (LFC). Increased adiposity in the HFC group, compared with the LFC group, was significantly (p<0.05) reduced in the HFG and HFGK groups without food intake being affected. Correlation network analysis, including a novel residuals analysis, was utilized to investigate relationships between liver proteomic data, lipid and cholesterol biomarkers and physiological indicators of adiposity. 6‐Gingerol significantly increased plasma cholesterol but hepatic farnesyl diphosphate synthetase, which is involved in cholesterol biosynthesis was decreased, possibly by negative feedback. Acetyl‐coenzyme A acyltransferase 1 and enoyl CoA hydratase, which participate in the β‐oxidation of fatty acids were significantly (p<0.05) increased by consumption of phytochemical‐supplemented diets.

Conclusion: Dietary ginger phytochemicals target cholesterol metabolism and fatty acid oxidation in mice, with anti‐obesogenic but also hypercholesterolemic consequences.
A food matrix reduces digestion and absorption of food allergens in vivo
Authors: Schulten Veronique , Lauer Iris , Scheurer Stephan , Thalhammer Theresia , Bohle Barbara
Published: September 2011

Scope: Food allergy is caused by primary (class 1) food allergens, e.g. Bos d 5 (cow's milk) and Cor a 8 (hazelnut) or secondary (class 2) food allergens, e.g. Mal d 1 (apple). The latter cannot sensitize susceptible individuals but can cause allergy due to immunological cross‐reactivity with homologous respiratory allergens. Here, we studied the effects of food matrix on gastrointestinal proteolysis, epithelial transport and in vivo absorption of class 1 and class 2 food allergens.

Methods and results: Mal d 1 lost its IgE‐reactivity immediately after simulated gastric digestion whereas Bos d 5 and Cor a 8 did not. Only Cor a 8 maintained IgE‐binding capacity after simulated intestinal proteolysis. The presence of hazelnut and peanut extracts, which served as protein‐rich model food matrices, delayed gastrointestinal degradation and reduced epithelial transport rates of all allergens through CaCo‐2 monolayers. Finally, IgE‐reactive allergens were assessed at different time points in sera from rats fed with all three allergens with or without hazelnut extract. The levels of all allergens peaked 2 h after animals were fed without matrix and increased over 8 h after feeding.

Conclusions: A protein‐rich food matrix delays gastrointestinal digestion and epithelial transport of food allergens and thereby may affect their sensitizing capacity and clinical symptoms.
Transitional states of acrosomal exocytosis and proteolytic processing of the acrosomal matrix in guinea pig sperm
Authors: Kim Kye‐Seong , Foster James A. , Kvasnicka Kevin W. , Gerton George L.
Published: September 2011

In this study, we adapted a FluoSphere bead‐binding assay to study the exposure and release of guinea pig sperm acrosomal components during the course of capacitation and acrosomal exocytosis. Prior to capacitation or the initiation of exocytosis, acrosomal proteins were not accessible to FluoSpheres coated with antibodies against two acrosomal matrix (AM) proteins, AM67 and AM50; during the course of capacitation and ionophore‐induced acrosomal exocytosis, however, we detected the transient exposure of the solid‐phase AM proteins on the surface of guinea pig sperm using the antibody‐coated fluorescent beads. Several different transitional stages leading to complete acrosomal exocytosis were classified, and we propose these represent true, functional intermediates since some of the AM proteins are orthologues of mouse proteins that bind the zona pellucida (ZP) of unfertilized eggs. In addition, we present evidence that implicates acrosin in the proteolytic processing of AM50 during AM disassembly. Thus, we propose that the transitional states of acrosomal exocytosis involve early binding of AM proteins to the ZP (by what visually appear to be “acrosome‐intact” sperm), maintenance of ZP binding that coincides with the progressive exposure of AM proteins, and gradual proteolytic disassembly of the AM to allow sperm movement through the ZP. We feel this “transitional states” model provides a more refined view of acrosomal function that supports a move away from the widely held, overly simplistic, and binary “acrosome‐reaction” model, and embraces a more dynamic view of acrosomal exocytosis that involves intermediate stages of the secretory process in ZP binding and penetration. Mol. Reprod. Dev. 78:930–941, 2011. © 2011 Wiley Periodicals, Inc.
Interobserver reproducibility of quantitative meniscus analysis using coronal multiplanar DESS and IWTSE MR imaging
Authors: Siorpaes Kristina , Wenger Andrea , Bloecker Katja , Wirth Wolfgang , Hudelmaier Martin , Eckstein Felix
Published: September 2011

The objective of this study was to determine the interobserver reproducibility of quantitative measures of meniscus size and position, and to compare the interobserver reproducibility and agreement between a double echo steady state water excitation and an intermediately‐weighted turbo spin‐echo sequence. Eight knees (four healthy, four with radiographic knee osteoarthritis) from the Osteoarthritis Initiative cohort were studied. Manual segmentation of the menisci was performed by three observers and quantitative measures of meniscus size and position (i.e., extrusion) computed using image analysis software. The root mean square interobserver reproducibility error (e.g., 5.4% for medial meniscus volume with double echo steady state and 8.4% with intermediately‐weighted turbo spin‐echo) was found considerably smaller than the intersubject variability (average ratio ∼1:3). The lowest interobserver reproducibility error for meniscus extrusion was obtained for the central five coronal slices across the tibial surface. Quantitative meniscus measures from double echo steady state and intermediately‐weighted turbo spin‐echo were highly correlated (r = 0.71 to 0.99 for the medial meniscus). Magn Reson Med, 2012. © 2011 Wiley Periodicals, Inc.
Superbalanced steady state free precession
Authors: Bieri Oliver
Published: September 2011

Steady state free precession (SSFP) signal theory is commonly derived in the limit of quasi‐instantaneous radiofrequency (RF) excitation. SSFP imaging protocols, however, are frequently set up with minimal pulse repetition times and RF pulses can thus constitute a considerable amount to the actual pulse repetition time. As a result, finite RF pulse effects can lead to 10–20% signal deviation from common SSFP theory in the transient and in the steady state which may impair the accuracy of SSFP‐based quantitative imaging techniques. In this article, a new and generic approach for intrinsic compensation of finite RF pulse effects is introduced. Compensation is based on balancing relaxation effects during finite RF excitation, similar to flow or motion compensation of gradient moments. RF pulse balancing, in addition to the refocusing of gradient moments with balanced SSFP, results in a superbalanced SSFP sequence free of finite RF pulse effects in the transient and in the steady state; irrespective of the RF pulse duration, flip angles, relaxation times, or off‐resonances. Superbalancing of SSFP sequences can be used with all quantitative SSFP techniques where finite RF pulse effects are expected or where elongated RF pulses are used. Magn Reson Med, 2012. © 2011 Wiley Periodicals, Inc.
Improved least squares MR image reconstruction using estimates of k‐Space data consistency
Authors: Johnson Kevin M. , Block Walter F. , Reeder Scott. B. , Samsonov Alexey
Published: September 2011

This study describes a new approach to reconstruct data that has been corrupted by unfavorable magnetization evolution. In this new framework, images are reconstructed in a weighted least squares fashion using all available data and a measure of consistency determined from the data itself. The reconstruction scheme optimally balances uncertainties from noise error with those from data inconsistency, is compatible with methods that model signal corruption, and may be advantageous for more accurate and precise reconstruction with many least squares‐based image estimation techniques including parallel imaging and constrained reconstruction/compressed sensing applications. Performance of the several variants of the algorithm tailored for fast spin echo and self‐gated respiratory gating applications was evaluated in simulations, phantom experiments, and in vivo scans. The data consistency weighting technique substantially improved image quality and reduced noise as compared to traditional reconstruction approaches. Magn Reson Med, 2011. © 2011 Wiley‐Liss, Inc.
Effects of B1 inhomogeneity correction for three‐dimensional variable flip angle T1 measurements in hip dGEMRIC at 3 T and 1.5 T
Authors: Siversson Carl , Chan Jenny , Tiderius Carl‐Johan , Mamisch Tallal Charles , Jellus Vladimir , Svensson Jonas , Kim Young‐Jo
Published: September 2011

Delayed gadolinium‐enhanced MRI of cartilage is a technique for studying the development of osteoarthritis using quantitative T1 measurements. Three‐dimensional variable flip angle is a promising method for performing such measurements rapidly, by using two successive spoiled gradient echo sequences with different excitation pulse flip angles. However, the three‐dimensional variable flip angle method is very sensitive to inhomogeneities in the transmitted B1 field in vivo. In this study, a method for correcting for such inhomogeneities, using an additional B1 mapping spin‐echo sequence, was evaluated. Phantom studies concluded that three‐dimensional variable flip angle with B1 correction calculates accurate T1 values also in areas with high B1 deviation. Retrospective analysis of in vivo hip delayed gadolinium‐enhanced MRI of cartilage data from 40 subjects showed the difference between three‐dimensional variable flip angle with and without B1 correction to be generally two to three times higher at 3 T than at 1.5 T. In conclusion, the B1 variations should always be taken into account, both at 1.5 T and at 3 T. Magn Reson Med, 2011. © 2011 Wiley‐Liss, Inc.
Power independent of number of slices (PINS) radiofrequency pulses for low‐power simultaneous multislice excitation
Authors: Norris David G. , Koopmans Peter J. , Boyacioğlu Rasim , Barth Markus
Published: September 2011

This communication describes radiofrequency pulses capable of performing spatially periodic excitation, inversion, and refocusing. The generation of such pulses either by multiplication of existing radiofrequency pulses by a Dirac comb function or by means of Fourier series expansion is described. Practical schemes for the implementation of such pulses are given, and strategies for optimizing the pulse profile at fixed pulse duration are outlined. The pulses are implemented using a spin‐echo sequence. The power deposition is independent of the number of slices acquired, and hence the power deposition per slice is considerably reduced compared to multislice imaging. Excellent image quality is obtained both in phantoms and in images of the human head. These pulses should find widespread application for multiplexed imaging, in particular at high static magnetic field strengths and for pulse sequences that have a high radiofrequency power deposition and could lead to dramatic increases in scanning efficiency. Magn Reson Med, 2011. © 2011 Wiley Periodicals, Inc.
Motion correction for myocardial T1 mapping using image registration with synthetic image estimation
Authors: Xue Hui , Shah Saurabh , Greiser Andreas , Guetter Christoph , Littmann Arne , Jolly Marie‐Pierre , Arai Andrew E , Zuehlsdorff Sven , Guehring Jens , Kellman Peter
Published: September 2011

Quantification of myocardial T1 relaxation has potential value in the diagnosis of both ischemic and nonischemic cardiomyopathies. Image acquisition using the modified Look‐Locker inversion recovery technique is clinically feasible for T1 mapping. However, respiratory motion limits its applicability and degrades the accuracy of T1 estimation. The robust registration of acquired inversion recovery images is particularly challenging due to the large changes in image contrast, especially for those images acquired near the signal null point of the inversion recovery and other inversion times for which there is little tissue contrast. In this article, we propose a novel motion correction algorithm. This approach is based on estimating synthetic images presenting contrast changes similar to the acquired images. The estimation of synthetic images is formulated as a variational energy minimization problem. Validation on a consecutive patient data cohort shows that this strategy can perform robust nonrigid registration to align inversion recovery images experiencing significant motion and lead to suppression of motion induced artifacts in the T1 map. Magn Reson Med, 2011. © 2011 Wiley‐Liss, Inc.
Recycling of 3He from lung magnetic resonance imaging
Authors: Salhi Z. , Großmann T. , Gueldner M. , Heil W. , Karpuk S. , Otten E. W. , Rudersdorf D. , Surkau R. , Wolf U.
Published: September 2011

We have developed the means to recycle 3He exhaled by patients after imaging the lungs using magnetic resonance of hyperpolarized 3He. The exhaled gas is collected in a helium leak proof bag and further compressed into a steel bottle. The collected gas contains about 1–2% of 3He, depending on the amount administered and the number of breaths collected to wash out the 3He gas from the lungs. 3He is separated from the exhaled air using zeolite molecular sieve adsorbent at 77 K followed by a cold head at 8 K. Residual gaseous impurities are finally absorbed by a commercial nonevaporative getter. The recycled 3He gas features high purity, which is required for repolarization by metastability exchange optical pumping. At present, we achieve a collection efficiency of 80–84% for exhaled gas from healthy volunteers and cryogenic separation efficiency of 95%. Magn Reson Med, 2011. © 2011 Wiley‐Liss, Inc.