bluuebunny/crossref_metadata_2025_split huggingface dataset:
Carcinogenesis, prevention and early detection of gastric cancer: Where we are and where we should go
Authors: González Carlos A. , Agudo Antonio 
Published: September 2011

AbstractHelicobacter pylori is the most common cause of gastric cancer (GC), though smoking, alcohol, diet, genetics and epigenetic factors may also have a role in the occurrence of the disease. Why H. pylori cause GC in only a minority of those infected remains unknown. Although mechanisms of H. pylori‐induced carcinogenesis are not yet well understood, several genotypes of H. pylori have been associated with strain virulence and disease risk. Primary prevention of GC should be addressed by avoiding exposure to factors that increase the risk and to promote factors associated with decrease risk. Vaccines against H. pylori are an ongoing promise and not yet available. Chemoprevention through vitamin supplementation has shown no benefit. Screening and eradication of H. pylori in the general population is not advised. Given that GC is a multiple‐steps process, the identification of patients with preneoplastic lesions with high risk of progression, and periodic endoscopic surveillance of them represents the most effective way for early diagnosis of GC. However, clinical guidelines for surveillance are lacking and there are no clear criteria to classify patients into high or low risk of progressing to GC. No study has shown the potential usefulness of combining the information on the type of preneoplastic lesions, genetic and epigenetic, lifestyle and virulence bacterial factors in order to identify high risk patients who need more intensive surveillance. The integration of all this information, in a prediction model requires further research and could be the most important contribution for reducing the burden of GC.
Differences in pathological and clinical features of breast cancer in Arab as compared to Jewish women in Northern Israel
Authors: Zidan Jamal , Sikorsky Natalya , Basher Walid , Sharabi Adi , Friedman Eitan , Steiner Mariana 
Published: September 2011

AbstractBreast cancer (BC) does not affect ethnic groups equally. BC mortality is higher in Israeli Palestinian Arab women than among Israeli Jewish women. This study aims to compare clinical, biological and pathological characteristics of breast cancer in the two populations. Records of 1,140 women with BC treated at Northern Israel between 2002 and 2007 were reviewed: 872 Jews and 268 Arabs. Age at diagnosis, tumor stage, pathological differentiation, estrogen receptor (ER) and HER‐2 expression were evaluated. The main age at diagnosis was 49.9 years for Arabs and 59.4 years for Jews (p < 0.0001). Mean tumor size was < 2 cm in 25% of Arabs and 53% of Jews (p < 0.0001). Lymph node metastases presented in 64.6% of Arabs and 37.2% of Jews (p < 0.0001). Stage I disease was 19% in Arab and 49.2% in Jewish women while Stages III and IV disease was 42% and 11.3% respectively (p < 0.001). ER was positive in 69% of Arabs and in 78.5% of Jews (p < 0.001). Poorly differentiated tumors were found in 28.8% of Arabs vs. 12.8% in Jews (p < 0.0001). Overexpression of HER‐2 was present in 35.4% of Arab and 22% of Jewish women (p < 0.001). We found that race is an important predictive factor for breast cancer. Arab women are diagnosed at younger age, with more advanced stage and biologically more aggressive disease than in Jewish women. Socioeconomic factors alone are not sufficient to explain significant effects of race on tumor characteristics. Findings suggest a different genetic susceptibility in the two populations which needs further research.
Chemical Synthesis of an Integral Membrane Enzyme — The Challenges of Diacylglycerol Kinase
Authors: Brehs Manuel , Bäuml Katja , Becker Christian F. W. 
Published: September 2011

AbstractAccess to integral membrane proteins via chemical synthesis or semisynthesis can provide detailed insights into the assembly and function of this diverse class of proteins. About one‐quarter to one‐third of all eukaryotic proteins are membrane proteins, and they fulfill a multitude of different functions as receptors and transducers for extracellular signals, as ion channels, and as scaffolds for large multi‐component assemblies. Many of these are still enigmatic and could benefit from synthetic access to these proteins, which allows almost unlimited variations of the peptide chain in order to address highly specific questions regarding their folding and function.The technical and synthetic challenges encountered during synthesis of these macromolecules are tremendous and help to drive the field of chemical protein synthesis beyond current limitations with respect to the ability to synthesize “difficult” hydrophobic sequences, purify them, and handle them in subsequent transformations, such as chemoselective ligation reactions.Here we provide an account of the synthetic challenges that we encountered en route to the first total chemical synthesis of an integral membrane protein comprising three membrane‐spanning domains: the E. coli diacylglycerol kinase. We hope this detailed description of our efforts will be helpful to others in tackling challenging protein synthesis targets.
YIELD AND WATER RELATIONS OF COTTON–MAIZE CROPPING SEQUENCE UNDER DEFICIT IRRIGATION USING DRIP SYSTEM
Authors: Sampathkumar T. , Pandian B. J. , Ranghaswamy M. V. , Manickasundaram P. 
Published: September 2011

ABSTRACTThe assessment of water use efficiency and crop performance of cotton–maize cropping sequence under deficit irrigation has not been thoroughly studied in India. Field experiments were conducted at the Agricultural College and Research Institute, Coimbatore, during 2007–2009 to study the effect of deficit irrigation practices through a drip irrigation system on crop productivity, and the water use efficiency of cotton–maize cropping sequence. Experimental treatments comprised of six irrigation levels (full and deficit) through a drip system, with surface irrigation as one of the treatments for comparison. Maize was sown after hybrid cotton, under no‐till conditions, without disturbing the raised bed and drip layout. Among deficit irrigation practices, mild deficit (ADI at 100% ETc once in three days) registered higher values for seed cotton yield (3670–3760 kg ha‐1), grain yield of maize (7420–7590 kg ha‐1) and water use efficiency (9.0 and 18.0–20.4 kg ha‐1 mm‐1 for cotton and maize, respectively). A significant second‐degree polynomial relationship between crop yields and water use (WU) was found for both the crops. Copyright © 2011 John Wiley & Sons, Ltd.
Direct and metabolism‐dependent cytochrome P450 inhibition assays for evaluating drug–drug interactions
Authors: Lee Kye Sook , Kim Sang Kyum 
Published: September 2011

ABSTRACTWe developed methods for evaluating the ntial inhibition of human cytochrome P450 (CYP) enzymes, including CYP1A2, CYP2A6, CYP2B6, CYP2 C9, CYP2 C19, CYP2D6, CYP2E1 and CYP3A4, using pooled human liver microsomes (HLMs). The CYP inhibition assay used substrate cocktail sets [set A: phenacetin for CYP1A2, coumarin for CYP2A6, (S)‐(+)‐mephenytoin for CYP2C19, dextromethorphan for CYP2D6 and midazolam for CYP3A4; set B: bupropion for CYP2B6, tolbutamide for CYP2C9, chlorzoxazone for CYP2E1, and testosterone for CYP3A4] with quantitation by liquid chromatography–tandem mass spectrometry. A direct inhibition assay was performed with the substrate cocktails without β‐nicotinamide adenine dinucleotide phosphate (NADPH) pre‐incubation, and a metabolism‐dependent inhibition (MDI) assay was performed after 30 min of pre‐incubation with NADPH in HLMs. MDI was identified based on the half‐maximal inhibitory concentration (IC50) shifts. The IC50 values of the direct inhibitors determined using the probe substrate cocktails were in good agreement with previously reported values. Eight metabolism‐dependent inhibitors including furafylline, 8‐methoxypsoralen, tienilic acid, ticlopidine, fluoxetine, paroxetine, disulfiram and verapamil against CYP1A2, CYP2A6, CYP2B6, CYP2C9, CYP2C19, CYP2D6, CYP2E1 and CYP3A4, respectively, resulted in significant IC50 shifts (≥2.5‐fold) after pre‐incubation. Thus, these CYP inhibition assays are considered to be useful tools for evaluating both direct inhibition and MDI at an early stage of the drug discovery and development process. Copyright © 2011 John Wiley & Sons, Ltd.
Applying efficient implicit nongeometric constraints in alchemical free energy simulations
Authors: Knight Jennifer L. , Brooks Charles L. 
Published: September 2011

AbstractSeveral strategies have been developed for satisfying bond lengths, angle, and other geometric constraints in molecular dynamics simulations. Advanced variations of alchemical free energy perturbation simulations, however, also require nongeometric constraints. In our recently developed multisite λ‐dynamics simulation method, the conventional λ parameters that are associated with the progress variables in alchemical transformations are treated as dynamic variables and are constrained such that: 0 ≤ λi ≤ 1 and ∑ λi = 1. Here, we present four functional forms of λ that implicitly satisfy these nongeometric constraints, whose values and forces are facile to compute and that yield stable simulations using a 2 fs integration timestep. Using model systems, we present the sampling characteristics of these functional forms and demonstrate the enhanced sampling profiles and improved convergence rates that are achieved by the functional form:
$\lambda _i = {{e^{c\sin \theta _i } } \over {\sum\nolimits_{j = 1}^N {e^{c\sin \theta _j } } }}$
that oscillates between λi = 0 and λi = 1 and has relatively steep transitions between these endpoints. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Randomized tree construction algorithm to explore energy landscapes
Authors: Jaillet Léonard , Corcho Francesc J. , Pérez Juan‐Jesús , Cortés Juan 
Published: September 2011

AbstractIn this work, a new method for exploring conformational energy landscapes is described. The method, called transition‐rapidly exploring random tree (T‐RRT), combines ideas from statistical physics and robot path planning algorithms. A search tree is constructed on the conformational space starting from a given state. The tree expansion is driven by a double strategy: on the one hand, it is naturally biased toward yet unexplored regions of the space; on the other, a Monte Carlo‐like transition test guides the expansion toward energetically favorable regions. The balance between these two strategies is automatically achieved due to a self‐tuning mechanism. The method is able to efficiently find both energy minima and transition paths between them. As a proof of concept, the method is applied to two academic benchmarks and the alanine dipeptide. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Assessment of in situ butanol recovery by vacuum during acetone butanol ethanol (ABE) fermentation
Authors: Mariano Adriano Pinto , Qureshi Nasib , Maciel Filho Rubens , Ezeji Thaddeus Chukwuemeka 
Published: September 2011

AbstractBACKGROUND: Butanol fermentation is product limiting owing to butanol toxicity to microbial cells. Butanol (boiling point: 118 °C) boils at a higher temperature than water (boiling point: 100 °C) and application of vacuum technology to integrated acetone–butanol–ethanol (ABE) fermentation and recovery may have been ignored because of direct comparison of boiling points of water and butanol. This research investigated simultaneous ABE fermentation using Clostridium beijerinckii 8052 and in situ butanol recovery by vacuum. To facilitate ABE mass transfer and recovery at fermentation temperature, batch fermentation was conducted in triplicate at 35 °C in a 14 L bioreactor connected in series with a condensation system and vacuum pump.RESULTS: Concentration of ABE in the recovered stream was greater than that in the fermentation broth (from 15.7 g L−1 up to 33 g L−1). Integration of the vacuum with the bioreactor resulted in enhanced ABE productivity by 100% and complete utilization of glucose as opposed to a significant amount of residual glucose in the control batch fermentation.CONCLUSION: This research demonstrated that vacuum fermentation technology can be used for in situ butanol recovery during ABE fermentation and that C. beijerinckii 8052 can tolerate vacuum conditions, with no negative effect on cell growth and ABE production. Copyright © 2011 Society of Chemical Industry
Bias in bacteriophage morphological classification by transmission electron microscopy due to breakage or loss of tail structures
Authors: Williamson Kurt E. , Helton Rebekah R. , Wommack K. Eric 
Published: September 2011

AbstractVirtually every study that has used transmission electron microscopy (TEM) to estimate viral diversity has acknowledged that loss of phage tails during sample preparation may have biased the results. However, the magnitude of this potential bias has yet to be constrained. To characterize biases in virus morphological diversity due to tail loss, six phage strains representing the order Caudovirales were inoculated into sterile sediments and soils. Phage particles were then extracted using standard methods. Morphologies of extracted phage particles were compared to those of unmanipulated control samples to determine the extent of tail breakage incurred by extraction procedures. Podoviruses exhibited the smallest frequency of tail loss during extraction (1.2–14%), myoviruses were moderately susceptible to tail breakage (15–40%), and siphoviruses were highly susceptible (32–76%). Thus, TEM assessments of viral diversity in soils or sediments by distribution of tail morphologies may be biased toward podoviruses and virions lacking tails, while simultaneously underestimating the abundance of siphoviruses. However, since the majority of viral capsids observed under TEM were intact, estimates of viral diversity based on the distribution of capsid diameters may provide a more reliable basis for morphological comparisons within and across ecosystems. Microsc. Res. Tech., 2011. © 2011 Wiley‐Liss, Inc.
Combination of transmission electron and atomic force microscopy techniques to determine volume equivalent diameter of submicrometer particles
Authors: Tumolva Laarnie , Park Ji‐Yeon , Park Kihong 
Published: September 2011

AbstractMorphological properties of atmospheric particles are directly related to their residence time and transport behaviors, and their deposition patterns in human respiratory systems. The projected properties of particles measured by transmission electron microscopy (TEM) were combined with the particle height measured by atomic force microscopy (AFM) to determine volume equivalent diameter of submicrometer particles. For nonvolatile (refractory) laboratory‐generated spherical polystyrene latex and cubic NaCl particles, the measured volume equivalent diameters agreed well with the true values (within 4%). However, for nonrefractory (NH4)2SO4 particles, the measured volume equivalent diameter was much smaller than the true value due to evaporation of volatile species at low vacuum pressure and high electron‐beam intensity conditions in TEM, and deformation of particles in AFM. We observed that the volume equivalent diameter of 100 nm mobility‐classified atmospheric particles was 35 ± 5 nm, suggesting that these particles contain nonrefractory species, whereas that of 20 nm mobility‐classified atmospheric particles was found to be 19 ± 6 nm, suggesting that these particles were refractory and spherical. Microsc. Res. Tech., 2011. © 2011 Wiley‐Liss, Inc.
Mechanisms of summertime precipitation variability in the Bolivian Altiplano: present and future
Authors: Thibeault Jeanne , Seth Anji , Wang Guiling 
Published: September 2011

AbstractWater availability is a major constraint to rural agriculture in the Bolivian Altiplano. The ability of medium and high‐resolution CMIP3 models to simulate observed relationships between interannual Altiplano summer precipitation anomalies and large‐scale patterns of precipitation, 200‐hPa winds and 200‐hPa geopotential height is examined. Altiplano precipitation anomalies are known to be related to upper‐level wind anomalies, with westerly (easterly) anomalies associated with deficit (excess) rainfall. A majority of models are able to simulate an easterly/wet‐westerly/dry relationship in response to changes in the zonal flow produced by fluctuations in tropical tropospheric temperatures that affect the meridional temperature gradient, consistent with observations.The 21st century evolution of these relationships under conditions of greenhouse warming is also examined. Results indicate that wet anomalies will continue to require moisture transport from the east. However, expected changes in mean circulation (e.g. tropical tropospheric warming) will likely influence precipitation variability. Models that better simulate Altiplano precipitation variability project an increase in 200‐hPa westerly winds by 2050–2099, which are not favourable for precipitation in the Altiplano. The reduced frequency of summertime upper‐level easterly wind anomalies may explain projections for less frequent summertime rainfall. Models that better simulate Altiplano precipitation variability project reduced summertime precipitation, consistent with projections for more frequent westerly wind anomalies. Summertime soil moisture reductions are expected from about 2020 onward due to reductions in summer rainfall, increases in the runoff ratio, higher evapotranspiration rates, and reduced precipitation frequency. These findings are consistent with expected large‐scale changes in atmospheric circulation, providing confidence in the projections. These results have serious implications for water resources and food security in the Altiplano, but will require further testing with improved, higher‐resolution models. Copyright © 2011 Royal Meteorological Society
Influence of different concentrations of 1‐methylcyclopropene on the quality of tomato harvested at different maturity stages
Authors: Sabir Ferhan K , Agar I Tayfun 
Published: September 2011

AbstractBACKGROUND: A wide range of 1‐methylcyclopropene (1‐MCP) concentrations as well as various treatment durations have been studied in tomatoes by different researchers. However, little is known about interaction of 1‐MCP doses and maturity stages of tomatoes. Therefore the effects of different concentrations of 1‐MCP on storage and postharvest quality of ‘Zorro’ tomatoes harvested at mature green or pink maturity stages were investigated in a 2‐year trial study.RESULTS: Higher concentrations of 1‐MCP delayed and/or inhibited all parameters related to fruit ripening, such as lycopene, chlorophyll, surface color, polygalacturonase (PG) activity and soluble solids content/titratable acidity (SSC/TA), and these effects were greater in tomatoes harvested at the mature green stages. Lower concentrations of 1‐MCP slightly reduced the loss in general quality features compared with untreated tomatoes.CONCLUSION: The results suggest that 1‐MCP, especially at higher doses, is effective for delaying ripening of mature green tomatoes. Mature green fruits treated with 1000 nL L−1 1‐MCP were stored for 35 days without significant decreases in quality characteristics such as elasticity, surface color and SSC/TA with certain physiological processes (ethylene production, PG activity, lycopene synthesis). Copyright © 2011 Society of Chemical Industry
Lipid metabolic effect of Korean red ginseng extract in mice fed on a high‐fat diet
Authors: Song Yong‐Bum , An Yu Ri , Kim Seung Jun , Park Hye‐Won , Jung Jin‐Wook , Kyung Jong‐Soo , Hwang Seung Yong , Kim Young‐Sook 
Published: September 2011

AbstractBACKGROUND: Ginseng saponin and ginsenosides exert anti‐obesity effects via the modulation of physiological lipid metabolism in vivo or intracellular signalling in cell culture systems. However, the complicated relationship between the anti‐obesity effects of ginseng and gene expression has yet to be defined under in vivo conditions. Therefore, we evaluated the relationship between the anti‐obesity effects of Korean red ginseng extract (KRGE) and hepatic gene expression profiles in mice fed long‐term on a high‐fat diet (HFD) in this study.RESULTS: KRGE reduces the levels of cholesterol, low‐density lipoprotein‐cholesterol (LDL‐C), serum triglycerides, and atherogenic indices. Levels of leptin, adiponectin and insulin, which regulate glucose and lipid metabolism, were impaired profoundly by HFD. However, KRGE treatment brought these levels back to normal. KRGE was found to down‐regulate genes associated with lipid metabolism or cholesterol metabolism (Lipa, Cyp7a1, Il1rn, Acot2, Mogat1, Osbpl3, Asah3l, Insig1, Anxa2, Vldlr, Hmgcs1, Sytl4, Plscr4, Pla2g4e, Slc27a3, Enpp6), all of which were up‐regulated by HFD.CONCLUSION: KRGE regulated the expression of genes associated with abnormal physiology via HFD. Leptin, insulin, and adiponectin, which carry out critical functions in energy and lipid metabolism, were shown to be modulated by KRGE. These results show that KRGE is effective in preventing obesity. Copyright © 2011 Society of Chemical Industry
Fat digestion and absorption in spice‐pretreated rats
Authors: Prakash Usha NS , Srinivasan Krishnapura 
Published: September 2011

AbstractBACKGROUND: A few common spices are known to stimulate secretion of bile with higher amount of bile acids which play a major role in digestion and absorption of dietary lipids. It would be appropriate to verify if these spices enable efficient digestion and absorption during high‐fat intake. In this context, dietary ginger (0.05%), piperine (0.02%), capsaicin (0.015%), and curcumin (0.5%) were examined for their influence on bile secretion, digestive enzymes of pancreas and absorption of dietary fat in high‐fat (30%) fed Wistar rats for 8 weeks.RESULTS: These spices enhanced the activity of pancreatic lipase, amylase, trypsin and chymotrypsin by 22‐57%, 32‐51%, 63‐81% and 12‐38%, respectively. Dietary intake of spices along with high‐fat enhanced fat absorption. These dietary spices increased bile secretion with higher bile acid content. Stimulation of lipid mobilisation from adipose tissue was suggested by the decrease in perirenal adipose tissue weight by dietary capsaicin and piperine. This was also accompanied by prevention of the accumulation of triglyceride in liver and serum in high‐fat fed rats. Activities of key lipogenic enzymes in liver were reduced which was accompanied by an increased activity of hormone‐sensitive lipase.CONCLUSION: Thus, dietary ginger and other spice compounds enhance fat digestion and absorption in high‐fat fed situation through enhanced secretion of bile salts and a stimulation of the activity pancreatic lipase. At the same time, the energy expenditure is facilitated by these spices to prevent the accumulation of absorbed fat. Copyright © 2011 Society of Chemical Industry