bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polymer‐based fluoride‐selective chemosensor: Synthesis, sensing property, and its use for the design of molecular‐scale logic devices
Authors: Lu Wei , Chen Dan , Jiang Han , Jiang Liming , Shen Zhiquan 
Published: November 2011

AbstractA new styryl‐type monomer, 2‐(4‐vinylbenzyloxy)‐1‐naphthaldehyde thiosemicarbazone (VNT), was synthesized and then copolymerized with methyl methacrylate (MMA) by reversible addition fragmentation chain transfer polymerization affording a series of poly(MMA‐co‐VNT)s with different functional unit content, predetermined molecular weight, and narrow molecular‐weight distribution. The desired copolymers were structurally confirmed by various spectroscopic characterizations. Colorimetric and fluorescent titration spectra revealed that the copolymers are highly selective toward fluoride anions over other competitive species including Cl−, Br−, I−, H2PO4−, AcO−, and HSO4−. On addition of F−, a remarkable colorless‐to‐yellow color change is easily observed by naked eyes. The influence of the copolymer composition and molecular weight on its sensing capacity was then carefully investigated. The results showed that higher VNT‐incorporation amount within the copolymer chains leads to higher sensitivity toward F− ions. Interestingly, the chromogenic process of the polymeric sensor can be switched back and forth by successively adding F− and HSO4− anions into the dimethyl sulfoxide solution of the polymer, which may be represented by a complementary “IMPLICATION/INHIBIT” logic gate at molecular level using both the ions as the chemical inputs. Based on such a reversible and reproducible sensing system, we designed a molecular‐scale sequential information processing circuit displaying “writing–reading–erasing–reading” behavior and “multiwrite” function in the form of binary logic. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Development of an ELISA to detect the secreted prostate cancer biomarker AGR2 in voided urine
Authors: Wayner Elizabeth A. , Quek Sue‐Ing , Ahmad Rumana , Ho Melissa E. , Loprieno Michelle A. , Zhou Yong , Ellis William J. , True Lawrence D. , Liu Alvin Y. 
Published: November 2011

AbstractBACKGROUNDComparative transcriptomics between sorted cells identified AGR2 as one of the highest up‐regulated genes in cancer. Overexpression in primary tumors was verified by tissue microarray analysis. AGR2 encodes a 19‐kDa secreted protein that might be found in urine.METHODSMonoclonal antibodies were generated against AGR2. One antibody pair, P1G4 (IgG1) to capture and P3A5 (IgG2a) to detect, showed good performance characteristics in a sandwich ELISA. This assay could detect AGR2 at sub ng/ml quantities.RESULTSAGR2 was detected in tissue digestion media of tumor specimens and culture media of AGR2‐secreting prostate cancer cell lines. Additional testings involved frozen section immunohistochemistry, immunoprecipitation, and Western blot analysis. Voided urine samples were collected from pre‐operative cancer patients, and urinary protein was desalted and concentrated by filtration. The amount of AGR2 detected was scored as pg/100 µg total protein, and then converted to pg/ml urine. The developed ELISA detected AGR2 protein, ranging from 3.6 to 181 pg/ml, in an initial cohort of samples. AGR2 was not detected in the urine of non‐cancer and a bladder cancer patient.CONCLUSIONSFor prostate cancer, an AGR2 urine test could be used for diagnosis. The data, although derived from a small number of samples assayed, showed that developing such a test for clinical application is viable because AGR2 is specific to cancer cells, and apparently secreted into urine. Prostate 72:1023–1034, 2012. © 2011 Wiley Periodicals, Inc.
Contrasting DNA damage checkpoint responses in epithelium of the human seminal vesicle and prostate
Authors: Jäämaa Sari , Sankila Anna , Rantanen Ville , Peltonen Karita , Järvinen Päivi M. , af Hällström Taija M. , Ruutu Mirja , Taari Kimmo , Andersson Leif C. , Laiho Marikki 
Published: November 2011

AbstractBACKGROUNDProstate and seminal vesicle are two similar hormone responsive human organs that differ dramatically in their cancer incidence. DNA damage response (DDR) is required for maintenance of genomic integrity.METHODSIn this study we investigated the DDR and cell cycle checkpoint activation of these organs using orthotopic cultures of human surgery‐derived tissues and primary cultures of isolated prostate and seminal vesicle cells.RESULTSWe find that the activation of ATM signaling pathway by ionizing radiation (IR) was comparable in both tissues. Previously, we have shown that the prostate secretory cells express low levels of histone variant H2AX and phosphorylated H2AX (γH2AX) after IR. Here we demonstrate that H2AX levels are low also in the secretory seminal vesicle cells suggesting that this is a common phenotype of postmitotic cells. We consequently established primary epithelial cell cultures from both organs to compare their DDR. Interestingly, contrary to human prostate epithelial cells (HPEC), primary seminal vesicle epithelial cells (HSVEC) displayed effective cell cycle checkpoints after IR and expressed higher levels of Wee1A checkpoint kinase. Furthermore, HSVEC but not HPEC cells were able to activate p53 and to induce p21 cell cycle inhibitor.DISCUSSIONOur results show that during replication, the checkpoint enforcement is more proficient in the seminal vesicle than in the prostate epithelium cells. This indicates a more stringent enforcement of DDR in replicating seminal vesicle epithelial cells, and suggests that epithelial regeneration combined with sub‐optimal checkpoint responses may contribute to high frequency of genetic lesions in the prostate epithelium. Prostate 72:1060–1070, 2012. © 2011 Wiley Periodicals, Inc.
Hexim‐1 modulates androgen receptor and the TGF‐β signaling during the progression of prostate cancer
Authors: Mascareno Eduardo J. , Belashov Ivan , Siddiqui M. A. Q. , Liu Fang , Dhar‐Mascareno Manya 
Published: November 2011

AbstractBACKGROUNDAndrogen and TGF‐β signaling are important components during the progression of prostate cancer. However, whether common molecular events participate in the activation of these signaling pathways are less understood.METHODHexim 1 expression was detected by immunohistochemistry of human tissue microarrays and TRAMP mouse models. The in vivo significance of Hexim‐1 was established by crossing the TRAMP mouse model of prostate cancer with Hexim‐1 heterozygous mice. TRAMP C2 cell line was also modified to delete one copy of Hexim‐1 gene to generate TRAMP‐C2‐Hexim‐1+/− cell lines.RESULTSIn this report, we observed that Hexim‐1 protein expression is absent in normal prostate but highly expressed in adenocarcinoma of the prostate and a characteristic sub‐cellular distribution among normal, benign hyperplasia, and adenocarcinoma of the prostate. Heterozygosity of the Hexim‐1 gene in the prostate cancer mice model and the TRAMP‐C2 cell line, leads to increased Cdk9‐dependent serine phosphorylation on protein targets such as the androgen receptor (AR) and the TGF‐β‐dependent downstream transcription factors, such as the SMAD proteins.CONCLUSIONOur results suggest that changes in the Hexim‐1 protein expression and cellular distribution significantly influences the AR activation and the TGF‐β signaling. Thus, Hexim‐1 is likely to play a significant role in prostate cancer progression. Prostate 72:1035–1044, 2012. © 2011 Wiley Periodicals, Inc.
Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization
Authors: Beuming Thijs , Che Ye , Abel Robert , Kim Byungchan , Shanmugasundaram Veerabahu , Sherman Woody 
Published: November 2011

AbstractWater plays an essential role in determining the structure and function of all biological systems. Recent methodological advances allow for an accurate and efficient estimation of the thermodynamic properties of water molecules at the surface of proteins. In this work, we characterize these thermodynamic properties and relate them to various structural and functional characteristics of the protein. We find that high‐energy hydration sites often exist near protein motifs typically characterized as hydrophilic, such as backbone amide groups. We also find that waters around alpha helices and beta sheets tend to be less stable than waters around loops. Furthermore, we find no significant correlation between the hydration site‐free energy and the solvent accessible surface area of the site. In addition, we find that the distribution of high‐energy hydration sites on the protein surface can be used to identify the location of binding sites and that binding sites of druggable targets tend to have a greater density of thermodynamically unstable hydration sites. Using this information, we characterize the FKBP12 protein and show good agreement between fragment screening hit rates from NMR spectroscopy and hydration site energetics. Finally, we show that water molecules observed in crystal structures are less stable on average than bulk water as a consequence of the high degree of spatial localization, thereby resulting in a significant loss in entropy. These findings should help to better understand the characteristics of waters at the surface of proteins and are expected to lead to insights that can guide structure‐based drug design efforts. Proteins 2011. © 2012 Wiley Periodicals, Inc.
On the T2 trap in zinc oxide thin films
Authors: Schmidt Matthias , Ellguth Martin , Karsthof Robert , v. Wenckstern Holger , Pickenhain Rainer , Grundmann Marius , Brauer Gerhard , Ling Francis C. C. 
Published: November 2011

AbstractWe investigated the electronic properties of the T2 deep‐level in zinc oxide thin films. It was found that T2 preferentially forms under zinc‐rich conditions and can be generated by either annealing the samples at reduced oxygen partial pressures ($p_{{\rm O}_{2} } < 1\;{\rm bar}$) or implanting zinc or copper ions, respectively. A strong dependence of its activation energy and high temperature limit of its cross‐section for electron capture on the T2 concentration in the sample is reported. Double DLTS measurements showed that the T2 activation energy decreases with increasing electric field due to phonon assisted tunnelling. Furthermore T2 can be photo‐ionised with a threshold photon energy of about 700 meV. Depth‐resolved concentration profiles of the T2 level in the samples were measured by optical capacitance–voltage spectroscopy.
Analyses on multiple resonance behaviors and microwave reflection loss in magnetic Co microflowers
Authors: Ma Zhi , Liu Qingfang , Yuan Jing , Wang Zhenkun , Cao Chentao , Wang Jianbo 
Published: November 2011

AbstractTriple dielectric and magnetic resonance behaviors have been observed and studied in Co microflowers within a frequency range of 0.1–18.0 GHz. To characterize such triple‐resonance behaviors, the dielectric resonance was resolved by fitting the Lorentzian dispersion law, magnetic resonance spectra was fitted by the Landau–Lifshitz–Gilbert equation. It is demonstrated that our fitted and calculated resonance frequencies agree well with the experimental data. Dielectric resonance in permittivity was due to the dipole polarization. Magnetic resonance in permeability was due to the natural/exchange resonance. Both the permittivity and permeability determined and contributed to the microwave reflection loss.
Double‐shell metamaterial coatings for plasmonic cloaking
Authors: Filonov Dmitry S. , Slobozhanyuk Alexey P. , Belov Pavel A. , Kivshar Yuri S. 
Published: November 2011

AbstractWe study a double‐shell cloak for hiding objects with the dimensions comparable with the radiation wavelength. We demonstrate that the structure consisting of a dielectric layer and a layer of an epsilon‐near‐zero material can suppress sub‐ stantially the scattering from a sphere and at the same time shield its interiors. The double‐layer coating allows to cloak different objects with various material and geometrical parameters. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Posttranscriptional Upregulation by MicroRNAs
Authors: Vasudevan Shobha 
Published: November 2011

AbstractMicroRNAs are small non‐coding RNA guide molecules that regulate gene expression via association with effector complexes and sequence‐specific recognition of target sites on other RNAs; misregulated microRNA expression and functions are linked to a variety of tumors, developmental disorders, and immune disease. MicroRNAs have primarily been demonstrated to mediate posttranscriptional downregulation of expression; translational repression, and deadenylation‐dependent decay of messages through partially complementary microRNA target sites in mRNA untranslated regions (UTRs). However, an emerging assortment of studies, discussed in this review, reveal that microRNAs and their associated protein complexes (microribonucleoproteins or microRNPs) can additionally function to posttranscriptionally stimulate gene expression by direct and indirect mechanisms. These reports indicate that microRNA‐mediated effects can be selective, regulated by the RNA sequence context, and associated with RNP factors and cellular conditions. Like repression, translation upregulation by microRNAs has been observed to range from fine‐tuning effects to significant alterations in expression. These studies uncover remarkable, new abilities of microRNAs and associated microRNPs in gene expression control and underscore the importance of regulation, in cis and trans, in directing appropriate microRNP responses. WIREs RNA 2012, 3:311–330. doi: 10.1002/wrna.121This article is categorized under:

Translation > Translation Mechanisms
Translation > Translation Regulation
Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms of Action
Ghrelin Agonist TZP‐101/Ulimorelin Accelerates Gastrointestinal Recovery Independently of Opioid Use and Surgery Type: Covariate Analysis of Phase 2 Data
Authors: Bochicchio Grant , Charlton Philippa , Pezzullo John C. , Kosutic Gordana , Senagore Anthony 
Published: November 2011

AbstractBackgroundDelayed recovery of gastrointestinal (GI) motility is a common complication following surgery. TZP‐101/ulimorelin is a macrocyclic peptidomimetic ghrelin receptor agonist with GI promotility effects that significantly accelerates time to recovery of GI motility compared to placebo following partial colectomy. It is also well tolerated. The objectives of this analysis were to identify predictors of GI motility recovery in patients undergoing partial colectomy and to evaluate whether these factors affect ulimorelin acceleration of GI recovery.MethodsCovariate analysis assessed the effect of eight variables—age, sex, body mass index, type of surgery (right colectomy, left colectomy, other), duration of surgery, blood loss, total opioid consumption, country—on recovery of GI motility in 236 patients randomized to ulimorelin (n = 168) or placebo (n = 68). The primary endpoint was the recovery of GI function (time from the end of surgery to first bowel movement). Stepwise regression identified a parsimonious model of the smallest subset of variables best predicting GI recovery.ResultsRecovery was shorter for segmental/subtotal colectomies vs. right colectomies (P = 0.016) and longer with increased total opioid use (P = 0.037). The remaining variables had no statistically significant effect on GI recovery. Effects of ulimorelin 480 μg/kg (the most effective dose) on time to GI tract recovery remained statistically and clinically significant (hazard ratio = 1.81, P = 0.014) when adjusted for surgery type and/or total opioid use.ConclusionsTwo factors, type of surgery and total opioid use, independently modified times to recovery of GI motility following partial large bowel resection surgery. Acceleration of recovery of GI motility by ulimorelin was independent of these factors.
Production of multiple extracellular enzyme activities by novel submerged culture of Aspergillus kawachii for ethanol production from raw cassava flour
Authors: Sugimoto Toshikazu , Makita Tomohiro , Watanabe Koutaro , Shoji Hiroshi 
Published: November 2011

Abstract
Cassava is a starch-containing root crop that is widely used as a raw material in a variety of industrial applications, most recently in the production of fuel ethanol. In the present study, ethanol production from raw (uncooked) cassava flour by simultaneous saccharification and fermentation (SSF) using a preparation consisting of multiple enzyme activities from Aspergillus kawachii FS005 was investigated. The multi-activity preparation was obtained from a novel submerged fermentation broth of A. kawachii FS005 grown on unmilled crude barley as a carbon source. The preparation was found to consist of glucoamylase, acid-stable α-amylase, acid carboxypeptidase, acid protease, cellulase and xylanase activities, and exhibited glucose and free amino nitrogen (FAN) production rates of 37.7 and 118.7 mg/l/h, respectively, during A. kawachii FS005-mediated saccharification of uncooked raw cassava flour. Ethanol production from 18.2% (w/v) dry uncooked solids of raw cassava flour by SSF with the multi-activity enzyme preparation yielded 9.0% (v/v) of ethanol and 92.3% fermentation efficiency. A feasibility study for ethanol production by SSF with a two-step mash using raw cassava flour and the multi-activity enzyme preparation manufactured on-site was verified on a pilot plant scale. The enzyme preparation obtained from the A. kawachii FS005 culture broth exhibited glucose and FAN production rates of 41.1 and 135.5 mg/l/h, respectively. SSF performed in a mash volume of about 1,612 l containing 20.6% (w/v) dry raw cassava solids and 106 l of on-site manufactured A. kawachii FS005 culture broth yielded 10.3% (v/v) ethanol and a fermentation efficiency of 92.7%.
Characterization of alginate lyase gene using a metagenomic library constructed from the gut microflora of abalone
Authors: Sim Su-Jung , Baik Keun Sik , Park Seong Chan , Choe Han Na , Seong Chi Nam , Shin Tai-Sun , Woo Hee Chul , Cho Jeong-Yong , Kim Duwoon 
Published: November 2011

Abstract
A metagenomic fosmid library was constructed using a genomic DNA mixture extracted from the gut microflora of abalone. The library gave an alginate lyase positive clone (AlyDW) harboring a 31.7-kbp insert. The AlyDW insert consisted of 22 open reading frames (ORFs). The deduced amino acid sequences of ORFs 11–13 were similar to those of known alginate lyase genes, which are found adjacent in the genome of Klebsiella pneumoniae subsp. aerogenes, Vibrio splendidus, and Vibrio sp. belonging to the phylum Gammaproteobacteria. Among the three recombinant proteins expressed from the three ORFs, alginate lyase activity was only observed in the recombinant protein (AlyDW11) coded by ORF 11. The expressed protein (AlyDW11) had the highest alginate lyase activity at pH 7.0 and 45°C in the presence of 1 mM AgNO3. The alginate lyase activity of ORF 11 was confirmed to be endolytic by thin-layer chromatography. AlyDW11 preferred poly(β-d-mannuronate) as a substrate over poly(α-l-guluronate). AlyDW11 contained three highly conserved regions, RSEL, QIH, and YFKAGVYNQ, which may act to stabilize the three-dimensional conformation and function of the alginate lyase.
Alginate production and alg8 gene expression by Azotobacter vinelandii in continuous cultures
Authors: Díaz-Barrera Alvaro , Soto Erik , Altamirano Claudia 
Published: November 2011

Abstract
Alginates are polysaccharides that are used as thickening agents, stabilizers, and emulsifiers in various industries. These biopolymers are produced by fermentation with a limited understanding of the processes occurring at the cellular level. The objective of this study was to evaluate the effects of agitation rate and inlet sucrose concentrations (ISC) on alginate production and the expression of the genes encoding for alginate-lyases (algL) and the catalytic subunit of the alginate polymerase complex (alg8) in chemostat cultures of Azotobacter vinelandii ATCC 9046. Increased alginate production (2.4 g l−1) and a higher specific alginate production rate (0.1 g g−1 h−1) were obtained at an ISC of 15 g l−1. Carbon recovery of about 100% was obtained at an ISC of 10 g l−1, whereas it was close to 50% at higher ISCs, suggesting that cells growing at lower sucrose feed rates utilize the carbon source more efficiently. In each of the steady states evaluated, an increase in algL gene expression was not related to a decrease in alginate molecular weight, whereas an increase in the molecular weight of alginate was linked to higher alg8 gene expression, demonstrating a relationship between the alg8 gene and alginate polymerization in A. vinelandii for the first time. The results obtained provide a possible explanation for changes observed in the molecular weight of alginate synthesized and this knowledge can be used to build a recombinant strain able to overexpress alg8 in order to produce alginates with higher molecular weights.
Cholesterol-lowering efficacy of a microencapsulated bile salt hydrolase-activeLactobacillus reuteriNCIMB 30242 yoghurt formulation in hypercholesterolaemic adults
Authors: Jones Mitchell L. , Martoni Christopher J. , Parent Mathieu , Prakash Satya 
Published: November 2011

Several studies have reported limited or no reduction in serum cholesterol in response to probiotic formulations. Recently, probiotics have shown promise in treating metabolic disease due to improved strain selection and delivery technologies. The aim of the present study was to evaluate the cholesterol-lowering efficacy of a yoghurt formulation containing microencapsulated bile salt hydrolase (BSH)-activeLactobacillus reuteriNCIMB 30242, taken twice per d over 6 weeks, in hypercholesterolaemic adults. A total of 114 subjects completed this double-blind, placebo-controlled, randomised, parallel-arm, multi-centre study. This interventional study included a 2-week washout, 2-week run-in and 6-week treatment period. Subjects were randomised to consume either yoghurts containing microencapsulatedL. reuteriNCIMB 30242 or placebo yoghurts. Over the intervention period, subjects consuming yoghurts containing microencapsulatedL. reuteriNCIMB 30242 attained significant reductions in LDL-cholesterol (LDL-C) of 8·92 % (P = 0·016), total cholesterol (TC) of 4·81 % (P = 0·031) and non-HDL-cholesterol (HDL-C) of 6·01 % (P = 0·029) over placebo, and a significant absolute change in apoB-100 of − 0·19 mmol/l (P = 0·049). Serum concentrations of TAG and HDL-C were unchanged over the course of the study. Present results show that consumption of microencapsulated BSH-activeL. reuteriNCIMB 30242 yoghurt is efficacious and safe for lowering LDL-C, TC, apoB-100 and non-HDL-C in hypercholesterolaemic subjects. The efficacy of microencapsulated BSH-activeL. reuteriNCIMB 30242 yoghurts appears to be superior to traditional probiotic therapy and akin to that of other cholesterol-lowering ingredients.