bluuebunny/crossref_metadata_2025 huggingface dataset:
Reefs and islands of the Chagos Archipelago, Indian Ocean: why it is the world's largest no‐take marine protected area
Authors: Sheppard C. R. C. , Ateweberhan M. , Bowen B. W. , Carr P. , Chen C. A. , Clubbe C. , Craig M. T. , Ebinghaus R. , Eble J. , Fitzsimmons N. , Gaither M. R. , Gan C‐H. , Gollock M. , Guzman N. , Graham N. A. J. , Harris A. , Jones R. , Keshavmurthy S. , Koldewey H. , Lundin C. G. , Mortimer J. A. , Obura D. , Pfeiffer M. , Price A. R. G. , Purkis S. , Raines P. , Readman J. W. , Riegl B. , Rogers A. , Schleyer M. , Seaward M. R. D , Sheppard A. L. S. , Tamelander J. , Turner J. R. , Visram S. , Vogler C. , Vogt S. , Wolschke H. , Yang J. M‐C. , Yang S‐Y. , Yesson C.
Published: January 2012

The Chagos Archipelago was designated a no‐take marine protected area (MPA) in 2010; it covers 550 000 km2, with more than 60 000 km2 shallow limestone platform and reefs. This has doubled the global cover of such MPAs.

It contains 25–50% of the Indian Ocean reef area remaining in excellent condition, as well as the world's largest contiguous undamaged reef area. It has suffered from warming episodes, but after the most severe mortality event of 1998, coral cover was restored after 10 years.

Coral reef fishes are orders of magnitude more abundant than in other Indian Ocean locations, regardless of whether the latter are fished or protected.

Coral diseases are extremely low, and no invasive marine species are known.

Genetically, Chagos marine species are part of the Western Indian Ocean, and Chagos serves as a ‘stepping‐stone’ in the ocean.

The no‐take MPA extends to the 200 nm boundary, and. includes 86 unfished seamounts and 243 deep knolls as well as encompassing important pelagic species.

On the larger islands, native plants, coconut crabs, bird and turtle colonies were largely destroyed in plantation times, but several smaller islands are in relatively undamaged state.

There are now 10 ‘important bird areas’, coconut crab density is high and numbers of green and hawksbill turtles are recovering.

Diego Garcia atoll contains a military facility; this atoll contains one Ramsar site and several ‘strict nature reserves’. Pollutant monitoring shows it to be the least polluted inhabited atoll in the world. Today, strict environmental regulations are enforced.

Shoreline erosion is significant in many places. Its economic cost in the inhabited part of Diego Garcia is very high, but all islands are vulnerable.

Chagos is ideally situated for several monitoring programmes, and use is increasingly being made of the archipelago for this purpose.

Copyright © 2012 John Wiley & Sons, Ltd.
Magnetic Gradient and Electrical Resistivity Tomography Surveys in Meroe, the Capital City of the Kush Kingdom, Sudan
Authors: Mohamed‐Ali M. A. , Herbich T. , Grzymski K. , Hobbs R.
Published: January 2012

One of the most important archaeological sites in Sudan is Meroe, capital city of the kingdom of Kush (800 bc to ad 400). The site is located in the Nile valley, about 200 km northeast of Khartoum. The most prominent feature among the ruins of Meroe is the Royal City: a stone‐walled enclosure containing remains of palaces, governmental buildings and temples. The current study presents the results of integrated magnetic gradient and electrical resistivity tomography surveys in unexplored and partly explored areas in the central part of the site and in the southern part of the Royal City. The main enclosure wall, remains of sandstone and red‐brick buildings, and a number of small archaeological structures have been traced on magnetic maps. The extent of buildings, identified by magnetic survey, has been complemented by information on the depth of structures provided by electrical resistivity tomography. The geophysical results have been partly verified through excavation. Copyright © 2012 John Wiley & Sons, Ltd.
Search effort degrades search output but improves task outcome
Authors: Vakkari Pertti , Huuskonen Saila
Published: January 2012

We analyzed how effort in searching is associated with search output and task outcome. In a field study, we examined how students' search effort for an assigned learning task was associated with precision and relative recall, and how this was associated to the quality of learning outcome. The study subjects were 41 medical students writing essays for a class in medicine. Searching in Medline was part of their assignment. The data comprised students' search logs in Medline, their assessment of the usefulness of references retrieved, a questionnaire concerning the search process, and evaluation scores of the essays given by the teachers. Pearson correlation was calculated for answering the research questions. Finally, a path model for predicting task outcome was built. We found that effort in the search process degraded precision but improved task outcome. There were two major mechanisms reducing precision while enhancing task outcome. Effort in expanding Medical Subject Heading (MeSH) terms within search sessions and effort in assessing and exploring documents in the result list between the sessions degraded precision, but led to better task outcome. Thus, human effort compensated bad retrieval results on the way to good task outcome. Findings suggest that traditional effectiveness measures in information retrieval should be complemented with evaluation measures for search process and outcome.
Hydrodynamic and kinetic study of cellulase production by Trichoderma reesei with pellet morphology
Authors: Yu Liang , Chao Yapeng , Wensel Pierre , Chen Shulin
Published: January 2012

Numerical simulations and experimental validation were performed to understand the effects of hydrodynamics on pellet formation and cellulase production by filamentous T. reesei. The constructed model combined a steady‐state multiple reference frame (MRF) approach describing mechanical mixing, oxygen mass transfer, and non‐Newtonian flow field with a transient sliding mesh approach and kinetics of oxygen consumption, pellet formation, and enzyme production. The model was experimentally validated at various agitation speeds in a two‐impeller Rushton turbine fermentor. Results from simulation and experimentation showed that higher agitation speeds led to increases in the pellet diameter and the proportion of pelletized (vs. filamentous) forms of the biomass. It also led to increase in dissolved oxygen mass transfer rate in shear‐thinning fluid and cellulase productivity. The extent of these increases varied considerably among agitation speeds. Pellet formation and morphology were presumably affected within a viscosity‐dependent shear‐rate range. Cellulase activity and cell viability were shown to be sensitive to impeller shear. A maximum cellulase activity of 3.5 IU/mL was obtained at 400 rpm, representing a twofold increase over that at 100 rpm. Biotechnol. Bioeng. 2012; 109:1755–1768. © 2012 Wiley Periodicals, Inc.
Debottlenecking recombinant protein production in Bacillus megaterium under large‐scale conditions—targeted precursor feeding designed from metabolomics
Authors: Korneli Claudia , Bolten Christoph Josef , Godard Thibault , Franco‐Lara Ezequiel , Wittmann Christoph
Published: January 2012

In the present work the impact of large production scale was investigated for Bacillus megaterium expressing green fluorescent protein (GFP). Specifically designed scale‐down studies, mimicking the intermittent and continuous nutrient supply of large‐ and small‐scale processes, were carried out for this purpose. The recombinant strain revealed a 40% reduced GFP yield for the large‐scale conditions. In line with extended carbon loss via formation of acetate and carbon dioxide, this indicated obvious limitations in the underlying metabolism of B. megaterium under the large‐scale conditions. Quantitative analysis of intracellular amino acids via validated fast filtration protocols revealed that their level strongly differed between the two scenarios. During cultivation in large‐scale set‐up, the availability of most amino acids, serving as key building blocks of the recombinant protein, was substantially reduced. This was most pronounced for tryptophan, aspartate, histidine, glutamine, and lysine. In contrast alanine was increased, probably related to a bottleneck at the level of pyruvate which also triggered acetate overflow metabolism. The pre‐cursor quantifications could then be exploited to verify the presumed bottlenecks and improve recombinant protein production under large‐scale conditions. Addition of only 5 mM tryptophan, aspartate, histidine, glutamine, and lysine to the feed solution increased the GFP yield by 100%. This rational concept of driving the lab scale productivity of recombinant microorganisms under suboptimal feeding conditions emulating large scale can easily be extended to other processes and production hosts. Biotechnol. Bioeng. 2012; 109:1538–1550. © 2012 Wiley Periodicals, Inc.
Glucose/O2 biofuel cell based on enzymes, redox mediators, and Multiple‐walled carbon nanotubes deposited by AC‐electrophoresis then stabilized by electropolymerized polypyrrole
Authors: Ammam Malika , Fransaer Jan
Published: January 2012

In this study, we developed an automated strategy to manufacture an enzyme BFC powered by glucose/O2. The bioanode consists of GOx enzyme and PQQ redox mediator adsorbed over night on MWCNTs then deposited by means of AC‐electrophoresis at 30 Hz and 160 Vp–p and, finally stabilized by electropolymerized polypyrrole. The biocathode is constructed from LAc enzyme and ABTS redox mediator adsorbed over night on MWCNTs, then electrophoretically deposited under AC‐electric field at 30 Hz and 160 Vp–p and, finally stabilized by electrodeposited polypyrrole. The BFC was studied under air in phosphate buffer solution pH 7.4 containing 10 mM glucose and in human serum with 5 mM glucose addition at the physiological temperature of 37°C. Under these conditions, the maximum power density reaches 1.1 µW · mm−2 at a cell voltage of 0.167 V in buffer solution and 0.69 µW · mm−2 at cell voltage of 0.151 V in human serum. Such automated BFCs have a great potential to be optimized, miniaturized to micro and nanoscale devices suitable for in vivo studies. Biotechnol. Bioeng. 2012; 109:1601–1609. © 2012 Wiley Periodicals, Inc.
BESSICC, a COSMO‐RS based tool for in silico solvent screening of biocatalyzed reactions
Authors: Braiuca P. , Khaliullin I. , Švedas V. , Knapic L. , Fermeglia M. , Halling P.J. , Gardossi L.
Published: January 2012

Many enzymatic reactions are near‐equilibrium reactions. This often limits final yield and hence application of biocatalyzed processes in the industrial production. The most widely applied strategy to overcome this issue is solvent selection. It must be underlined that measuring the equilibrium position experimentally is a difficult and time‐consuming procedure and any tool for predicting the solvent effect on the reaction equilibrium can be very valuable. The present work reports on the development of BESSICC, an algorithm to calculate the effect of medium composition on biocatalyzed reactions equilibrium. It is based on COSMO‐RS calculation of activity coefficients of all the species in the reaction mixture and minimization of Gibbs free energy of the reaction. Starting from one single experimental measurement of the equilibrium position for a given biocatalyzed reaction it can predict the yield of the reaction in any other solvent or solvent mixture. Predictions are accurate, the errors of prediction are in average below 25% for the esterification of dodecanoic acid with menthol and below 65% for esterification of 1‐dodecanoic acid with 1‐dodecanol. The best predictions show an error well below 5%. Biotechnol. Bioeng. 2012; 109:1864–1868. © 2012 Wiley Periodicals, Inc.
Continuum heterogeneous biofilm model—A simple and accurate method for effectiveness factor determination
Authors: Gonzo Elio Emilio , Wuertz Stefan , Rajal Veronica B.
Published: January 2012

We present a novel analytical approach to describe biofilm processes considering continuum variation of both biofilm density and substrate effective diffusivity. A simple perturbation and matching technique was used to quantify biofilm activity using the steady‐state diffusion–reaction equation with continuum variable substrate effective diffusivity and biofilm density, along the coordinate normal to the biofilm surface. The procedure allows prediction of an effectiveness factor, η, defined as the ratio between the observed rate of substrate utilization (reaction rate with diffusion resistance) and the rate of substrate utilization without diffusion limitation. Main assumptions are that (i) the biofilm is a continuum, (ii) substrate is transferred by diffusion only and is consumed only by microorganisms at a rate according to Monod kinetics, (iii) biofilm density and substrate effective diffusivity change in the x direction, (iv) the substrate concentration above the biofilm surface is known, and (v) the substratum is impermeable. With this approach one can evaluate, in a fast and efficient way, the effect of different parameters that characterize a heterogeneous biofilm and the kinetics of the rate of substrate consumption on the behavior of the biological system. Based on a comparison of η profiles the activity of a homogeneous biofilm could be as much as 47.8% higher than that of a heterogeneous biofilm, under the given conditions. A comparison of η values estimated for first order kinetics and η values obtained by numerical techniques showed a maximum deviation of 1.75% in a narrow range of modified Thiele modulus values. When external mass transfer resistance, is also considered, a global effectiveness factor, η0, can be calculated. The main advantage of the approach lies in the analytical expression for the calculation of the intrinsic effectiveness factor η and its implementation in a computer program. For the test cases studied convergence was achieved quickly after four or five iterations. Therefore, the simulation and scale‐up of heterogeneous biofilm reactors can be easily carried out. Biotechnol. Bioeng. 2012; 109:1779–1790. © 2012 Wiley Periodicals, Inc.
Differential in‐gel electrophoresis (DIGE) analysis of CHO cells under hyperosmotic pressure: Osmoprotective effect of glycine betaine addition
Authors: Kim Jee Yon , Kim Yeon‐Gu , Lee Gyun Min
Published: January 2012

The use of glycine betaine combined with hyperosmolality is known to be an efficient means for achieving high protein production in recombinant Chinese hamster ovary (rCHO) cells. In order to understand the intracellular events and identify the key factors in rCHO cells cultivated with glycine betaine under hyperosmotic conditions, two‐dimensional differential in‐gel electrophoresis (2D‐DIGE) followed by mass spectrometric analysis was applied. Differentially expressed 19 protein spots were selected and 16 different kinds of proteins were successfully identified. The identified proteins were associated with cellular metabolism (PEPCK, GAPDH, and PK), cellular architecture (β‐tubulin and β‐actin), protein folding (GRP78 and OSP94), mRNA processing (Rbm34, ACF, and IPMK), and protein secretion (γ‐COP). 2D‐Western blot analysis of β‐tubulin, GAPDH, Peroxidoxin‐1, and GRP78 confirmed the proteomic findings. The proteins identified from this study, which are related to cell growth and antibody production, can be applied to cell engineering for maximizing the efficacy of the use of glycine betaine combined with hyperosmolality in rCHO cells. Biotechnol. Bioeng. 2012; 109:1395–1403. © 2012 Wiley Periodicals, Inc.
Topographic cues of nano‐scale height direct neuronal growth pattern
Authors: Baranes Koby , Chejanovsky Nathan , Alon Noa , Sharoni Amos , Shefi Orit
Published: January 2012

We study the role of nano‐scale cues in controlling neuronal growth. We use photolithography to fabricate substrates with repeatable line‐pattern ridges of nano‐scale heights. We find that neuronal processes, which are of micron size, have strong interactions with ridges even as low as 10 nm. The interaction between the neuronal process and the ridge leads to a deflection of growth direction and a preferred alignment with the ridges. The interaction strength clearly depends on the ridges' height. For 25 nm ridges approximately half of the neuronal processes are modified, while at 100 nm the majority of neurites change their original growth direction post interaction. In addition, the effect on growth correlates with the incoming angle between the neuronal process and the ridge. We underline the adhesion as a key mechanism in directing neuronal growth. Our study highlights the sensitivity of growing neurites to nano‐scale cues thus opens a new avenue of research for pre‐designed neuronal growth and circuitry. Biotechnol. Bioeng. 2012; 109:1791–1797. © 2012 Wiley Periodicals, Inc.
Generation of a cholesterol‐independent, non‐GS NS0 cell line through chemical treatment and application for high titer antibody production
Authors: Li Jincai , Gu Wei , Edmondson Diane G. , Lu Connie , Vijayasankaran Natarajan , Figueroa Bruno , Stevenson Dave , Ryll Thomas , Li Feng
Published: January 2012

NS0 cells require exogenous cholesterol for growth. The non‐glutamine synthetase (GS) cholesterol‐dependent NS0 host was treated with 5‐azacytidine (5azaC), a demethylation drug, and adapted to grow in cholesterol‐free, chemically defined medium. Within 7 weeks, a stable, cholesterol‐independent NS0 host (NS0.CF) was obtained. The new NS0.CF host, as well as the original cholesterol auxotroph host, was transfected with the same mAb expression plasmid, and the top producing clone from both hosts were compared side‐by‐side in the enhanced platform fed‐batch cultures using chemically defined media. The NS0.CF derived clone significantly out‐performed the cholesterol‐dependent clone, with titer reaching 4.5 g/L versus 3.0 g/L, respectively, mainly due to higher specific productivity, while key product quality attributes remained comparable. This work demonstrated an effective and rapid approach to generate a cholesterol‐independent NS0 host, and its application in recombinant protein production. Biotechnol. Bioeng. 2012; 109:1685–1692. © 2012 Wiley Periodicals, Inc.
Differentiation of PC12 cells in three‐dimensional collagen sponges with micropatterned nerve growth factor
Authors: Oh Hwan Hee , Lu Hongxu , Kawazoe Naoki , Chen Guoping
Published: January 2012

Micropatterning of biological cues is important for the guided formation of neuronal outgrowth and neuronal differentiation. Nerve growth factor (NGF) was micropatterned in a three‐dimensional collagen sponges by using micropatterned ice lines that were composed of collagen and NGF. The micropatterned ice lines were prepared by a dispersing machine. PC12 cells were cultured in the NGF‐micropatterned collagen sponges and showed micropatterned neurite outgrowth. The neurite outgrowth followed the micropattern of NGF with more neurite outgrowth in the collagen/NGF lines than in the regions between the collagen/NGF lines. The micropattern of the NGF and the neurite network of the PC12 cells can be manipulated by controlling the micropattern of the NGF. The three‐dimensional porous scaffolds prepared by this method will have a potential application for the regeneration and repair of the nervous system. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2012
Chemical Constituents and Some Biological Activities of Plants from the Genus Ceriops
Authors: Wang Hui , Li Min‐Yi , Wu Jun
Published: January 2012

In this review, the literature data on phytochemical and biological investigations of the genus Ceriops are compiled. The Ceriops species are mangrove plants widely distributed along the sea coasts of Africa, Madagascar, South Asia, and South Pacific islands. To date, 43 diterpenes and 29 triterpenes have been reported from the embryos, fruits, hypocotyls, roots, stems, and twigs of C. tagal and C. decandra. Diterpenoids and triterpenoids are the main constituents of this genus. The isolated terpenes showed an enormous structural diversity and exhibited various biological properties, such as antitumor, antibacterial, and larvicidal activities.
Phenolic Compounds from the Branches of Eucalyptus maideni
Authors: Tian Li‐Wen , Xu Min , Li Yan , Li Xing‐Yao , Wang Dong , Zhu Hong‐Tao , Yang Chong‐Ren , Zhang Ying‐Jun
Published: January 2012

Three new phenolic compounds, eucalmaidin F (1), (3S)‐5‐guaiacyl‐3‐hydroxypentanoic acid (2), and 8‐β‐C‐glucopyranosyl‐5,7‐dihydroxy‐2‐isobutylchromone (3), were isolated from the branches of E. maideni, together with 30 known compounds, including four phenylpropanoids, three lignans, four phloroglucinol glucosides, five dihydroflavonoids, seven simple phenolic compounds, six terpenoids, and glycerol. The new structures were established by spectroscopic studies (MS, and 1D‐ and 2D‐NMR), chemical degradation, and modified Mosher's method. Compounds 3, guaiacylglycerol, 3‐hydroxy‐1‐(4‐hydroxyphenyl)propan‐1‐one, caffeic acid, (2E)‐3‐(4‐hydroxyphenyl)prop‐2‐enoic acid, (7′S,8R,8′R)‐lyoniresinol, (+)‐lyoresinol 3α‐O‐α‐L‐rhamnopyranoside, garcimangosone, phlorocetophenone 2′‐glucopyranoside, (+)‐taxifolin 3α‐O‐α‐L‐rhamnopyranoside, (+)‐aromadendrin, (+)‐taxifolin, resveratrol, piceatannol, 3,4,5‐trihydroxyphenol. Tachiaside, gallic acid, macrocapals A und G, and oleuropeic acid were evaluated for their cytotoxicities against five human cancer cell lines. Resveratrol, piceatannol, gallic acid, and macrocapal G exhibited moderate inhibitory effects on human myeloid heukemia HL‐60 cell, with IC50 values of 22.05, 22.05, 7.75, and 31.93 μM, respectively; and only macrocapal G showed inhibitory effect on hepatocellular carcinoma SMMC‐7721 cell, with an IC50 value of 26.75 μM.
Inhibitory Effects of Terpenoids from the Fermented Broth of the Ascomycete Stilbohypoxylon elaeicola YMJ173 on Nitric Oxide Production in RAW264.7 Macrophages
Authors: Wang Guei‐Jane , Liang Wen‐Li , Ju Yu‐Ming , Yang Wen‐Bin , Chang Ya‐Wen , Lee Tzong‐Huei
Published: January 2012

A series of six isopimarane‐type diterpene glycosides, along with an eremophilane‐type sesquiterpene, i.e., elaeicolasides A–C (1–3, resp.), 16‐(α‐D‐mannopyranosyloxy)isopimar‐7‐en‐19‐oic acid (4), hymatoxin K (5), hymatoxin L (6), and elaeicolalactone (7), were isolated from the AcOEt extract of the fermented broth of Stilbohypoxylon elaeicola YMJ173. Among these, 1–3 and 7 are new compounds based on their spectroscopic data and sugar composition analysis. The effects of 1–7 on the inhibition of nitric oxide (NO) production in lipopolysaccharide (LPS)‐activated murine macrophage RAW264.7 cells were evaluated. All these compounds inhibited NO production, detected as nitrite in the culture medium, in activated macrophages without any cytotoxicity at a concentration of 100 μM. Among these compounds, 2 showed a significant activity with the average maximum inhibition (Emax) and median inhibitory concentration (IC50) values of 93.3±0.5% and 79.3±0.4 μM, respectively.
Studies of the Activity of Peroxidase‐Like DNAzyme by Modifying 3′‐ or 5′‐End of Aptamers
Authors: Zhang Ming , Li Haiqun , Deng Minggang , Weng Xiaocheng , Ma Heng , Feng Shuo , Zhou Yangyang , Zhou Xiang
Published: January 2012

In the presence of hemin and under appropriate conditions, some modalities of G‐quadruplexes can form a peroxidase‐like DNAzyme that has been widely used in biology. Structurefunction studies on the DNAzyme revealed that its catalytic ability may be dependent on the unimolecular parallel G‐quadruplex. In this report, we present the preliminary investigation on the relationship between the structure and function of DNAzymes through a terminal oligo modification in G‐quadruplex sequences by adding different lengths of oligo‐dT to the 3′‐ or 5′‐end of the aptamers. The results suggested that adding dTn to the 5′‐end of the DNA sequence of the enzyme improved the ability of hemin to bind with DNA, but the addition of dTn to the 3′‐end decreased the binding ability of hemin for DNA. The increased stability of the assembled DNAzyme would lead to more favorable binding between the enzyme and substrate (H2O2), facilitating higher peroxidase activity; on the contrary, with lower stability of the DNAzyme complex, we observed reduced peroxidase activity.
Essential Oils in the Ranunculaceae Family: Chemical Composition of Hydrodistilled Oils from Consolida regalis, Delphinium elatum, Nigella hispanica, and N. nigellastrum Seeds
Authors: Kokoska Ladislav , Urbanova Klara , Kloucek Pavel , Nedorostova Lenka , Polesna Lucie , Malik Jan , Jiros Pavel , Havlik Jaroslav , Vadlejch Jaroslav , Valterova Irena
Published: January 2012

In this study, we analyzed the chemical composition of volatile oils hydrodistilled from seeds of Consolida regalis, Delphinium elatum, Nigella hispanica, and N. nigellastrum using GC and GC/MS. In C. regalis, octadecenoic (77.79%) and hexadecanoic acid (8.34%) were the main constituents. Similarly, the oils from D. elatum and N. hispanica seeds consisted chiefly of octadecadienoic (42.83 and 35.58%, resp.), hexadecanoic (23.87 and 28.59%, resp.), and octadecenoic acid (21.67 and 19.76%, resp.). Contrastingly, the monoterpene hydrocarbons α‐pinene (34.67%) and β‐pinene (36.42%) were the main components of N. nigellastrum essential oil. Our results confirm the presence of essential oils in the family Ranunculaceae and suggest chemotaxonomical relationships within the representatives of the genera Consolida, Delphinium, and Nigella. In addition, the presence of various bioactive constituents such as linoleic acid, (−)‐β‐pinene, squalene, or carotol in seeds of D. elatum, N. hispanica, and N. nigellastrum indicates a possible industrial use of these plants.
Effects of insulin and insulin‐like growth factor 1 on osteoblast proliferation and differentiation: differential signalling via Akt and ERK
Authors: Zhang Wei , Shen Xing , Wan Chao , Zhao Qiang , Zhang Lianfang , Zhou Qi , Deng Lianfu
Published: January 2012

Insulin and insulin‐like growth factor 1 (IGF‐1) are evolutionarily conserved hormonal signalling molecules, which influence a wide array of physiological functions including metabolism, growth and development. Using genetic mouse studies, both insulin and IGF‐1 have been shown to be anabolic agents in osteoblasts and bone development primarily through the activation of Akt and ERK signalling pathways. In this study, we examined the temporal signalling actions of insulin and IGF‐1 on primary calvarial osteoblast growth and differentiation. First, we observed that the IGF‐1 receptor expression decreases whereas insulin receptor expression increases during osteoblast differentiation. Subsequently, we show that although both insulin and IGF‐1 promote osteoblast differentiation and mineralization in vitro, IGF‐1, but not insulin, can induce osteoblast proliferation. The IGF‐1‐induced osteoblast proliferation was mediated via both MAPK and Akt pathways because the IGF‐1‐mediated cell proliferation was blocked by U0126, an MEK/MAPK inhibitor, or LY294002, a PI3‐kinase inhibitor. Osteocalcin, an osteoblast‐specific protein whose expression corresponds with osteoblast differentiation, was increased in a dose‐ and time‐dependent manner after insulin treatment, whereas it was decreased with IGF‐1 treatment. Moreover, insulin treatment dramatically induced osteocalcin promoter activity, whereas IGF‐1 treatment significantly inhibited it, indicating direct effect of insulin on osteocalcin synthesis. Copyright © 2012 John Wiley & Sons, Ltd.
Effects of indoleamine 2,3‐dioxygenases in carbon tetrachloride‐induced hepatitis model of rats
Authors: Li Dan , Cai Haidong , Hou Min , Fu Da , Ma Yushui , Luo Qiong , Yuan Xueyu , Lv Mingli , Zhang Xiaoping , Cong Xianling , Lv Zhongwei
Published: January 2012

Indoleamine 2,3‐dioxygenase (IDO) converts tryptophan to l‐kynurenine, and it is noted as a relevant molecule in promoting tolerance and suppressing adaptive immunity. In this study, to investigate the effects of IDO in carbon tetrachloride (CCl4)–induced hepatitis model, the levels of IDO enzymic activities in the mock group, the control group and the 1‐methyl‐d‐tryptophan (1‐MT)–treated group were confirmed by determination of l‐kynurenine concentrations. Serum alanine aminotransferase levels in 1‐MT‐treated rats after CCl4 injection significantly increased compared with those in mock and control groups. In CCl4‐induced hepatitis models, tumour necrosis factor‐α (TNF‐α) is critical in the development of liver injury. The mRNA expression and secretion levels of TNF‐α in the liver from 1‐MT‐treated rats were more enhanced compared with those in the mock and the control groups. Moreover, the levels of cytokine and chemokine from mock, control group and 1‐MT‐treated rats after treated with CCl4 were analyzed by ELISA, and the level of interleukin‐6 was found to increase in 1‐MT‐treated rats. It was concluded that the deficiency of IDO exacerbated liver injury in CCl4‐induced hepatitis and its effect may be connected with TNF‐α and interleukin‐6. Copyright © 2012 John Wiley & Sons, Ltd.
P‐bodies and their functions during mRNA cell cycle: Mini‐review
Authors: Olszewska Marta , Bujarski Józef J. , Kurpisz Maciej
Published: January 2012

P‐bodies (processing bodies) are observed in different organisms such as yeast, Caenorhabditis elegans and mammals. A typical eukaryotic cell contains several types of spatially formed granules, such as P‐bodies, stress granules and a variety of ribonucleoprotein bodies. These microdomains play important role in mRNA processing, including RNA interference, repression of translation and mRNA decay. The P‐bodies components as well as stress granules may play an important role in host defense against viral infection. The complete set of P‐bodies protein elements is still poor known. They contain conserved protein core limited to different organisms or to stress status of the cell. P‐bodies are related also to some neuronal mRNA granules as well as to maternal RNA granules or male germ cell granules. In this mini‐review, we focus on the structure of P‐bodies and their function in the mRNA utilization and processing because of the high mRNA's dynamics between different cellular compartments and its key role in modulation of gene expression. Copyright © 2012 John Wiley & Sons, Ltd.
The Importance of Peripheral Sequences in Determining the Metal Selectivity of an in Vitro‐Selected Co2+‐Dependent DNAzyme
Authors: Nelson Kevin E. , Ihms Hannah E. , Mazumdar Debapriya , Bruesehoff Peter J. , Lu Yi
Published: January 2012

DNAzymes are catalytically active DNA molecules that use metal cofactors for their enzymatic functions. While a growing number of DNAzymes with diverse functions and metal selectivities have been reported, the relationships between metal ion selectivity, conserved sequences and structures responsible for selectivity remain to be elucidated. To address this issue, we report biochemical assays of a family of previously reported in vitro selected DNAzymes. This family includes the clone 11 DNAzyme, which was isolated by positive and negative selection, and the clone 18 DNAzyme, which was isolated by positive selection alone. The clone 11 DNAzyme has a higher selectivity for Co2+ over Pb2+ compared with clone 18. The reasons for this difference are explored here through phylogenetic comparison, mutational analysis and stepwise truncation. A novel DNAzyme truncation method incorporated a nick in the middle of the DNAzyme to allow for truncation close to the nicked site while preserving peripheral sequences at both ends of the DNAzyme. The results demonstrate that peripheral sequences within the substrate binding arms, most notably the stem loop, loop II, are sufficient to restore its selectivity for Co2+ over Pb2+ to levels observed in clone 11. A comparison of these sequences' secondary structures and Co2+ selectivities suggested that metastable structures affect metal ion selectivity. The Co2+ selectivity of the clone 11 DNAzyme showed that the metal ion binding and selectivities of small, in vitro selected DNAzymes may be more complex than previously appreciated, and that clone 11 may be more similar to larger ribozymes than to other small DNAzymes in its structural complexity and behavior. These factors should be taken into account when metal‐ion selectivity is required in rationally designed DNAzymes and DNAzyme‐based biosensors.
Mixed Colloidal Suspensions of Reduced Graphene Oxide and Layered Metal Oxide Nanosheets: Useful Precursors for the Porous Nanocomposites and Hybrid Films of Graphene/Metal Oxide
Authors: Lee Yu Ri , Kim In Young , Kim Tae Woo , Lee Jang Mee , Hwang Seong‐Ju
Published: January 2012

Homogeneously mixed colloidal suspensions of reduced graphene oxide, or RGO, and layered manganate nanosheets have been synthesized by a simple addition of the exfoliated colloid of RGO into that of layered MnO2. The obtained mixed colloidal suspensions with the RGO/MnO2 ratio of ≤0.3 show good colloidal stability without any phase separation and a negatively charged state with a zeta (ζ) potential of −30 to −40 mV. The flocculation of these mixed colloidal suspensions with lithium cations yields porous nanocomposites of Li/RGO‐layered MnO2 with high electrochemical activity and a markedly expanded surface area of around 70–100 m2 g−1. Relative to the Li/RGO and Li/layered MnO2 nanocomposites (≈116 and ≈167 F g−1), the obtained Li/RGO‐layered MnO2 nanocomposites deliver a larger capacitance of approximately 210 F g−1 with good cyclability of around 95–97 % up to the 1000th cycle, thus indicating the positive effect of hybridization on the electrode performances of RGO and lithium manganate. Also, an electrophoretic deposition of the mixed colloidal suspensions makes it possible to easily fabricate uniform hybrid films composed of graphene and manganese oxide. The obtained films show a distinct electrochemical activity and a homogeneous distribution of RGO and MnO2. The present experimental findings clearly demonstrate that the utilization of the mixed colloidal suspensions as precursors provides a facile and universal methodology to synthesize various types of graphene/metal oxide hybrid materials.
Routine clinical use of the one‐step nucleic acid amplification assay for detection of sentinel lymph node metastases in breast cancer patients
Authors: Tamaki Yasuhiro , Sato Nobuaki , Homma Keiichi , Takabatake Daisuke , Nishimura Rieko , Tsujimoto Masahiko , Yoshidome Katsuhide , Tsuda Hitoshi , Kinoshita Takayuki , Kato Hironori , Taniyama Kiyomi , Kamio Takako , Nakamura Seigo , Akiyama Futoshi , Noguchi Shinzaburo ,   and the Japanese One‐Step Nucleic Acid Amplification Study Group
Published: January 2012

BACKGROUND:

The objective of this study was to confirm, by means of a multicenter study conducted in Japan, the reliability and usefulness of the one‐step nucleic acid amplification (OSNA) assay in routine clinical use for sentinel lymph node biopsy (SLNB) of breast cancer patients.

METHODS:

Patients with Tis‐T2N0M0 breast cancer who underwent SLNB before systemic chemotherapy comprised the study cohort. A whole sentinel lymph node (SLN) was examined intraoperatively with the OSNA assay except for a 1‐mm‐thick, central slice of the lymph node, which underwent pathologic examination after the operation. For patients who underwent axillary dissection, non‐SLNs were examined with routine pathologic examination.

RESULTS:

In total, 417 SLNBs from 413 patients were analyzed. SLN metastases were detected with greater sensitivity by the OSNA assay than by pathologic examination (22.5% vs 15.8%; P < .001), as expected from the difference in size of the specimens examined. Patients who had SLN metastases assessed with the OSNA assay proved to harbor non‐SLN metastases with an overall risk ratio of 33.7%. The risk of non‐SLN metastasis was significantly lower for patients who had positive SLNs assessed as OSNA+ than for those who had SLNs assessed as OSNA++ (17.6% vs 44%; P = .012).

CONCLUSIONS:

The OSNA assay can be used for routine clinical SLNB, and its assessment for volume of metastasis may be a powerful predictive factor for non‐SLN metastasis. Further studies with more patients are needed to confirm the usefulness of this assay for selection in the clinical setting of patients who do not need axillary dissection. Cancer 2012;3477–3483. © 2012 American Cancer Society.
Limited‐stage diffuse large B‐cell lymphoma treated with abbreviated systemic therapy and consolidation radiotherapy
Authors: Campbell Belinda A. , Connors Joseph M. , Gascoyne Randy D. , Morris W. James , Pickles Tom , Sehn Laurie H.
Published: January 2012

BACKGROUND:

For limited‐stage diffuse large B‐cell lymphoma (DLBCL), treatment decisions are often influenced by toxicity profiles. One strategy that minimizes chemotherapy‐induced toxicities is abbreviated chemotherapy plus consolidation involved‐field radiotherapy (IFRT). Involved‐node radiotherapy (INRT) is a new concept to DLBCL, aimed to reduce radiotherapy‐induced toxicities. We retrospectively review the long‐term outcomes of limited‐stage DLBCL treated with abbreviated systemic therapy and radiotherapy focusing on field size: IFRT versus INRT.

METHODS:

The British Columbia Cancer Agency Lymphoid Cancer Database was used to identify patients diagnosed with limited‐stage DLBCL (stage I/II, without B‐symptoms; bulk < 10 cm) from 1981 to 2007. Patients were prescribed 3 cycles of chemotherapy plus IFRT (1981‐1996) or INRT≤5 cm (1996‐2007), defined as INRT to the prechemotherapy involved nodes with margins ≤ 5 cm.

RESULTS:

A total of 288 patients were identified: 56% were aged >60 years, 34% had stage II disease, 55% had extranodal disease, 19% had elevated lactate dehydrogenase levels, and 15% received rituximab. The two radiotherapy groups were IFRT (138 patients; 48%) and INRT≤5cm (150 patients; 52%); median follow‐up was 117 and 89 months, respectively. Distant relapse was the most common site of failure in both groups. After INRT≤5 cm, marginal recurrence was infrequent (2%). Time to progression (P = .823), progression‐free survival (P = .575), and overall survival (P = .417) were not significantly different between the radiotherapy cohorts. Radiotherapy field size was not a significant prognostic factor on multivariate analyses.

CONCLUSIONS:

This research is the first known body of work to apply the concept of INRT to limited‐stage DLBCL. Reducing the field size from IFRT to INRT≤5 cm maintains a low marginal recurrence risk with no impact on overall outcome. Cancer 2012. © 2012 American Cancer Society.
Gene expression identifies heterogeneity of metastatic propensity in high‐grade soft tissue sarcomas
Authors: Skubitz Keith M. , Francis Princy , Skubitz Amy P. N. , Luo Xianghua , Nilbert Mef
Published: January 2012

BACKGROUND:

Metastatic propensity of soft tissue sarcoma (STS) is heterogeneous and may be determined by gene expression patterns that do not correlate well with morphology. The authors have reported gene expression patterns that distinguish 2 broad classes of clear cell renal carcinoma (ccRCC‐gene set), and other patterns that can distinguish heterogeneity of serous ovarian carcinoma (OVCA‐gene set) and aggressive fibromatosis (AF‐gene set); however, clinical follow‐up data were not available for these samples.

METHODS:

In the current study, gene expression patterns in 73 samples of high‐grade STS were examined using spotted cDNA microarray slides that contained ∼16,000 unique UniGene clusters. Approximately 50% of the genes present in the ccRCC‐, OVCA‐, and AF‐gene sets were also represented in the data from this chip set, and these were combined to form a composite gene set of 278 probes.

RESULTS:

Hierarchical clustering using this composite gene set suggested the existence of subsets of the STS samples. Analysis revealed differences in the time to development of metastatic disease between the clusters defined by the first branch point of the clustering dendrogram (P = .005), and also among the 4 different clusters defined by the second branch points (P = .001).

CONCLUSIONS:

This approach suggests the existence of >2 subsets of high‐grade pleomorphic STS, each with distinct clinical behavior. A composite gene set such as that described here may be useful to stratify STS in clinical trials, and may be of practical utility in patient management. Cancer 2012. © 2012 American Cancer Society.
Associations among physical activity, body mass index, and health‐related quality of life by race/ethnicity in a diverse sample of breast cancer survivors
Authors: Paxton Raheem J. , Phillips Karon L. , Jones Lovell A. , Chang Shine , Taylor Wendell C. , Courneya Kerry S. , Pierce John P.
Published: January 2012

BACKGROUND:

Health‐related quality of life (HRQOL), body mass index (BMI), and physical activity (PA) levels have all been associated with prognosis following breast cancer and may explain partially the higher mortality for breast cancer in certain racial/ethnic subgroups. In this study, associations between PA, BMI, and HRQOL by race were examined in a sample of breast cancer survivors.

METHODS:

Measures of PA, BMI, and HRQOL as well as demographic and medical characteristics of women (N = 3013, 13% nonwhite) who participated in the Women's Healthy Eating and Living Study were assessed at baseline. Analysis of covariance was used to examine the relationship between PA and obesity with HRQOL outcomes. Statistical tests were 2‐sided.

RESULTS:

African American women were less likely to meet guidelines for PA and more likely to be obese than women from other ethnic groups (P < .05). In adjusted models, women who met guidelines for PA reported significantly higher physical health composite (point differences ranged from 10.5 to 21.2 points, all P < .05) and vitality (point differences ranged from 9.9 to 16.5 points, all P < .05) scores than those who did not, regardless of race/ethnicity. Associations between obesity and HRQOL were mixed with fewer associations for Asian American and African American women and stronger associations for whites.

CONCLUSIONS:

Breast cancer survivors from racially and ethnically diverse populations have lower levels of PA and higher rates of obesity that are generally associated with poorer HRQOL. Culturally sensitive PA and weight loss interventions may improve these lifestyle characteristics and result in improved HRQOL. Cancer 2012. © 2012 American Cancer Society.
Outcome after ipsilateral breast tumor recurrence in patients who receive accelerated partial breast irradiation
Authors: Shah Chirag , Vicini Frank , Keisch Martin , Kuerer Henry , Beitsch Peter , Haffty Bruce , Lyden Maureen
Published: January 2012

BACKGROUND:

The objective of this study was to examine clinical outcomes and patterns of failure in patients with early stage breast cancer who developed an ipsilateral breast tumor recurrence (IBTR) after breast‐conserving therapy (BCT) using accelerated partial breast irradiation (APBI).

METHODS:

In total, 1440 patients (1449 tumors) with early stage breast cancer who underwent BCT were treated with the MammoSite device to deliver APBI (34 Gray [Gy] in 3.4‐Gy fractions). One thousand two hundred fifty‐five patients (87%) had invasive breast cancer (IBC) (median tumor size, 10 mm), and 194 patients (13%) had ductal carcinoma in situ (DCIS) (median tumor size, 8 mm). The median follow‐up was 60 months.

RESULTS:

Fifty patients (3.5%) developed an IBTR for a 5‐year actuarial rate of 3.61% (3.65% for IBC and 3.36% for DCIS). It was determined that 36 recurrences (72%) represented new primary cancers, and 14 recurrences (28%) represented recurrences of the index lesion. Of the 32 recurrences with known histology, 78% were IBC, and 22% were DCIS. After IBTR, 28 of 38 patients (74%) underwent salvage mastectomy, and 9 of 38 patients (26%) had a second attempt at BCT. Adjuvant therapies included tamoxifen in 8 patients (16%) and systemic chemotherapy in 6 patients (12%). The 3‐year rates of disease‐free survival, cause‐specific survival, and overall survival after IBTR were 58.7%, 92.1%, and 80.5%, respectively.

CONCLUSIONS:

With 5 years of follow‐up, APBI produced clinical outcomes and patterns of failure comparable to those achieved with whole breast irradiation. Patients who developed an IBTR after APBI had excellent 3‐year survival outcomes after salvage treatments. Cancer 2012. © 2012 American Cancer Society.
Radiation therapy at the end of life in patients with incurable nonsmall cell lung cancer
Authors: Kapadia Nirav S. , Mamet Rizvan , Zornosa Carrie , Niland Joyce C. , D'Amico Thomas A. , Hayman James A.
Published: January 2012

BACKGROUND:

Receipt of chemotherapy at the end of life (EOL) is considered an indicator of poor quality of care for medical oncology. The objective of this study was to characterize the use of radiotherapy (RT) in patients with nonsmall cell lung cancer (NSCLC) during the same period.

METHODS:

Treatment characteristics of patients with incurable NSCLC who received RT at the EOL, defined as within 14 days of death, were analyzed from the National Comprehensive Cancer Network NSCLC Outcomes Database.

RESULTS:

Among 1098 patients who died, 10% had received EOL RT. Patients who did and did not receive EOL RT were similar in terms of sex, race, comorbid disease, and Eastern Cooperative Oncology Group performance status. On multivariable logistic regression analysis, independent predictors of receiving EOL RT included stage IV disease (odds ratio [OR], 2.04; 95% confidence interval [CI], 1.09‐3.83) or multiorgan involvement (OR, 1.75; 95% CI, 1.08‐2.84) at diagnosis, age <65 years at diagnosis (OR, 1.85; 95% CI, 1.21‐2.83), and treating institution (OR, 1.24‐5.94; P = .02). Nearly 50% of EOL RT recipients did not complete it, most commonly because of death or patient preference.

CONCLUSIONS:

In general, EOL RT was received infrequently, was delivered more commonly to younger patients with more advanced disease, and often was not completed as planned. There also was considerable variation in its use among National Comprehensive Cancer Network institutions. Next steps include expanding this research to other cancers and settings and investigating the clinical benefit of such treatment. Cancer 2012. © 2012 American Cancer Society.
Computational model of soft tissues in the human upper airway
Authors: Pelteret J‐P. V. , Reddy B. D.
Published: January 2012

This paper presents a three‐dimensional finite element model of the tongue and surrounding soft tissues with potential application to the study of sleep apnoea and of linguistics and speech therapy. The anatomical data was obtained from the Visible Human Project, and the underlying histological data was also extracted and incorporated into the model. Hyperelastic constitutive models were used to describe the material behaviour, and material incompressibility was accounted for. An active Hill three‐element muscle model was used to represent the muscular tissue of the tongue. The neural stimulus for each muscle group was determined through the use of a genetic algorithm‐based neural control model. The fundamental behaviour of the tongue under gravitational and breathing‐induced loading is investigated. It is demonstrated that, when a time‐dependent loading is applied to the tongue, the neural model is able to control the position of the tongue and produce a physiologically realistic response for the genioglossus. Copyright © 2012 John Wiley & Sons, Ltd.
Human skull shape and masticatory induced stress: Objective comparison through the use of non‐rigid registration
Authors: Jansen van Rensburg Gerhardus J. , Wilke Daniel N. , Kok Schalk
Published: January 2012

Variation in masticatory induced stress, caused by shape changes in the human skull, is quantified in this article. A comparison on masticatory induced stress is presented subject to a variation in human skull shape. Non‐rigid registration is employed to obtain appropriate computational domain representations. This procedure allows the isolation of shape from other variations that could affect the results. An added benefit, revealed through the use of non‐rigid registration to acquire appropriate domain representation, is the possibility of direct and objective comparison and manipulation. The effect of mapping uncertainty on the direct comparison is also quantified. As shown in this study, exact difference values are not necessarily obtained, but a non‐rigid map between subject shapes and numerical results gives an objective indication on the location of differences. Copyright © 2012 John Wiley & Sons, Ltd.