bluuebunny/crossref_metadata_2025_split huggingface dataset:
Counter‐Anion Effect on the Properties of Anion‐Conducting Polymer Electrolyte Membranes Prepared by Radiation‐Induced Graft Polymerization
Authors: Koshikawa Hiroshi , Yoshimura Kimio , Sinnananchi Warapon , Yamaki Tetsuya , Asano Masaharu , Yamamoto Kazuya , Yamaguchi Susumu , Tanaka Hirohisa , Maekawa Yasunari 
Published: July 2013

AbstractGraft‐type anion‐conducting polymer electrolyte membranes (AEMs) are prepared by the radiation‐induced graft polymerization of chloromethylstyrene into poly(ethylene‐co‐tetrafluoroethylene) (ETFE) films and subsequent quaternization with trimethylamine. AEMs in the hydroxide form (AEM‐OH) are prepared by immersing the chloride form (AEM‐Cl) in 1 M potassium hydroxide (KOH) solution, followed by KOH and washing with nitrogen‐saturated water to prevent bicarbonate formation (AEM‐HCO3). The AEM‐OH shows conductivity and water uptake four and two times higher than AEM‐Cl and ‐HCO3 and is thermally and chemically less stable, resulting in the tendency to absorb water and to convert to the bicarbonate form.magnified image
Purification and characterization of transcription factors
Authors: Nagore L.I. , Nadeau R.J. , Guo Q. , Jadhav Y.L.A. , Jarrett H.W. , Haskins W.E. 
Published: July 2013

AbstractTranscription factors (TFs) are essential for the expression of all proteins, including those involved in human health and disease. However, TFs are resistant to proteomic characterization because they are frequently masked by more abundant proteins due to the limited dynamic range of capillary liquid chromatography‐tandem mass spectrometry and protein database searching. Purification methods, particularly strategies that exploit the high affinity of TFs for DNA response elements (REs) on gene promoters, can enrich TFs prior to proteomic analysis to improve dynamic range and penetrance of the TF proteome. For example, trapping of TF complexes specific for particular REs has been achieved by recovering the element DNA–protein complex on solid supports. Additional methods for improving dynamic range include two‐ and three‐dimensional gel electrophoresis incorporating electrophoretic mobility shift assays and Southwestern blotting for detection. Here we review methods for TF purification and characterization. We fully expect that future investigations will apply these and other methods to illuminate this important but challenging proteome. © 2013 Wiley Periodicals, Inc. Rapid Commun. Mass Spectrom. 32: 386–398, 2013.
Microbial diversity in the floral nectar of sevenEpipactis(Orchidaceae) species
Authors: Jacquemyn Hans , Lenaerts Marijke , Tyteca Daniel , Lievens Bart 
Published: July 2013

AbstractFloral nectar of animal‐pollinated plants is commonly infested with microorganisms, yet little is known about the microorganisms inhabiting the floral nectar of orchids. In this study, we investigated microbial communities occurring in the floral nectar of sevenEpipactis(Orchidaceae) species. Culturable bacteria and yeasts were isolated and identified by partially sequencing the small subunit (SSU) ribosomal RNA (rRNA) gene and the D1/D2 domains of the large subunit (LSU) rRNA gene, respectively. Using three different culture media, we found that bacteria were common inhabitants of the floral nectar ofEpipactis. The most widely distributed bacterial operational taxonomic units (OTUs) in nectar ofEpipactiswere representatives of the family of Enterobacteriaceae,with an unspecified Enterobacteriaceae bacterium as the most common. In contrast to previous studies investigating microbial communities in floral nectar, very few yeast species (mainly of the genusCryptococcus) were observed, and most of them occurred in very low densities. Total OTU richness (i.e., the number of bacterial and yeast OTUs per orchid species) varied between 4 and 20. Cluster analysis revealed that microbial communities of allogamous species differed from those of autogamous and facultatively autogamous species. This study extends previous efforts to identify microbial communities in floral nectar and indicates that the floral nectar of the orchids investigated mainly contained bacterial communities with moderate phylogenetic diversity.
Neuropathy and levodopa in Parkinson's disease: Evidence from a multicenter study
Authors: Ceravolo Roberto , Cossu Giovanni , Bandettini di Poggio Monica , Santoro Lucio , Barone Paolo , Zibetti Maurizio , Frosini Daniela , Nicoletti Valentina , Manganelli Fiore , Iodice Rosa , Picillo Marina , Merola Aristide , Lopiano Leonardo , Paribello Alessandra , Manca Davide , Melis Maurizio , Marchese Roberta , Borelli Paolo , Mereu Alessandra , Contu Paolo , Abbruzzese Giovanni , Bonuccelli Ubaldo 
Published: July 2013

ABSTRACTThe objectives of this study were to evaluate the risk of neuropathy in patients with Parkinson's disease (PD) and to evaluate the role of levodopa exposure as a potential risk factor. A multicenter study of 330 patients with PD and 137 healthy controls with a comparable age distribution was performed. With respect to levodopa exposure, 144 patients had long exposure (≥3 years) to levodopa (LELD), 103 patients had short exposure (<3 years) to levodopa (SELD), and 83 patients had no exposure to levodopa (NOLD). Nerve function was evaluated using the reduced total neuropathy score. Right sural sensory antidromic and peroneal motor nerve conduction studies were performed by neurophysiologists who were blinded to the existence of neuropathy clinical features or PD treatment. Overall, 19.40% of patients in the LELD group, 6.80% in the SELD group, 4.82% in the NOLD group, and 8.76% in the control group were diagnosed with neuropathy (axonal, predominantly sensory). Multivariate logistic analysis indicated that the risk of neuropathy was not influenced by disease duration, severity, or sex. The risk of neuropathy increased by approximately 8% for each year of age (P < 0.001; odds ratio [OR], 1.08; 95% confidence interval [CI], 1.037‐1.128). The risk of neuropathy was 2.38 higher in the LELD group than in the control group (P = 0.022; OR, 2.38; 95% CI, 1.130‐5.014). In a comparison between patients with and without neuropathy (Student's t test), the levodopa dose was higher (P < 0.0001), serum vitamin B12 levels were lower (P = 0.0102), and homocysteine levels were higher (P < 0.001) in the patients with neuropathy. Our results demonstrate that the duration of exposure to levodopa, along with age, is the main risk factor for the development of neuropathy. Screening for homocysteine and vitamin B12 levels and clinical‐neurophysiological monitoring for neuropathy may be advisable in patients with PD who are receiving treatment with levodopa. © 2013 International Parkinson and Movement Disorder Society
Nicotine reduces established levodopa‐induced dyskinesias in a monkey model of Parkinson's disease
Authors: Quik Maryka , Mallela Archana , Ly Jason , Zhang Danhui 
Published: July 2013

ABSTRACTAlthough 3,4‐dihydroxyphenylalanine (levodopa) is the gold‐standard treatment for Parkinson's disease, it can lead to disabling dyskinesias. Previous work demonstrated that nicotine reduces levodopa‐induced dyskinesias (LIDs) in several parkinsonian animal models. The goal of this study was to determine whether the duration of nicotine administration affects its ability to reduce LIDs in levodopa‐primed and levadopa‐naíve monkeys and also to test whether tolerance develops to the beneficial effects of nicotine. Monkeys were injected with MPTP (1.9‐2.0 mg/kg subcutaneously) over 3 to 5 months until parkinsonism developed. Nicotine (300 μg/mL) was administered in drinking water (over 4–6 months) to levodopa‐primed or levodopa‐naíve monkeys, with levodopa/carbidopa (10/2.5 mg/kg) gavaged twice daily. One set of MPTP‐lesioned monkeys (n = 23) was first gavaged with levodopa and subsequently received nicotine 4 weeks later, when dyskinesias plateaued, or 8 weeks later, when dyskinesias were established. A 60% to 70% decrease in LIDs was observed after several weeks of nicotine treatment in both groups. A second set of monkeys (n = 26) received nicotine 8 or 2 weeks before levodopa. In the 8‐week nicotine pretreatment group, there was an immediate reduction in LIDs, which plateaued at 60% to 70%. In the 2‐week nicotine pretreatment group, there were initial small decreases in LIDs, which plateaued at 60% to 70% several weeks later. Thus, nicotine pretreatment and nicotine post‐treatment were similarly efficacious in reducing LIDs. The beneficial effect of nicotine persisted throughout the study (17–23 weeks). Nicotine did not worsen parkinsonism. These data suggest that nicotine treatment has potential as a successful antidyskinetic therapy for patients with Parkinson's disease. © 2013 International Parkinson and Movement Disorder Society
Identification of novel point mutations in splicing sites integrating whole‐exome and RNA‐seq data in myeloproliferative diseases
Authors: Spinelli Roberta , Pirola Alessandra , Redaelli Sara , Sharma Nitesh , Raman Hima , Valletta Simona , Magistroni Vera , Piazza Rocco , Gambacorti‐Passerini Carlo 
Published: July 2013

AbstractPoint mutations in intronic regions near mRNA splice junctions can affect the splicing process. To identify novel splicing variants from exome sequencing data, we developed a bioinformatics splice‐site prediction procedure to analyze next‐generation sequencing (NGS) data (SpliceFinder). SpliceFinder integrates two functional annotation tools for NGS, ANNOVAR and MutationTaster and two canonical splice site prediction programs for single mutation analysis, SSPNN and NetGene2. By SpliceFinder, we identified somatic mutations affecting RNA splicing in a colon cancer sample, in eight atypical chronic myeloid leukemia (aCML), and eight CML patients. A novel homozygous splicing mutation was found in APC (NM_000038.4:c.1312+5G>A) and six heterozygous in GNAQ (NM_002072.2:c.735+1C>T), ABCC3 (NM_003786.3:c.1783‐1G>A), KLHDC1 (NM_172193.1:c.568‐2A>G), HOOK1 (NM_015888.4:c.1662‐1G>A), SMAD9 (NM_001127217.2:c.1004‐1C>T), and DNAH9 (NM_001372.3:c.10242+5G>A). Integrating whole‐exome and RNA sequencing in aCML and CML, we assessed the phenotypic effect of mutations on mRNA splicing for GNAQ, ABCC3, HOOK1. In ABCC3 and HOOK1, RNA‐Seq showed the presence of aberrant transcripts with activation of a cryptic splice site or intron retention, validated by the reverse transcription‐polymerase chain reaction (RT‐PCR) in the case of HOOK1. In GNAQ, RNA‐Seq showed 22% of wild‐type transcript and 78% of mRNA skipping exon 5, resulting in a 4–6 frameshift fusion confirmed by RT‐PCR. The pipeline can be useful to identify intronic variants affecting RNA sequence by complementing conventional exome analysis.
Rough Set Theory as an Interpretable Method for Predicting the Inhibition of Cytochrome P450 1A2 and 2D6
Authors: Burton Julien , Petit Joachim , Danloy Emeric , Maggiora Gerald M. , Vercauteren Daniel P. 
Published: July 2013

AbstractEarly prediction of ADME properties such as the cytochrome P450 (CYP) mediated drug‐drug interactions is an important challenge in the drug discovery area. In this study, we propose to couple an original data mining approach based on Rough Set Theory (RST) to a structural description of molecules. The latter was achieved by using two types of structural keys: (1) the MACCS keys and (2) a set of five in‐house fingerprints based on properties of the electron density distributions of chemical groups. The compounds considered are involved in the inhibition of CYP1A2 and CYP2D6. RST allowed the extraction of rules further used as classifiers to predict the inhibitory profile of an independent set of molecules. The results reached prediction accuracies of 90.6 and 88.2 % for CYP1A2 and CYP2D6, respectively. In addition, these classifiers were analyzed to determine which structural fragments were most used for building the rules, revealing relationships between the occurrence of particular molecular fragments and CYP inhibition. The results assessed RST as a suitable tool to build strongly predictive models and infer structure‐activity rules associated with potency.
Targeted induction of endogenous NKX3‐1 by small activating RNA inhibits prostate tumor growth
Authors: Ren Shancheng , Kang Moo Rim , Wang Ji , Huang Vera , Place Robert F. , Sun Yinhao , Li Long‐Cheng 
Published: July 2013

AbstractBACKGROUNDRNA activation (RNAa) is a small RNA‐mediated gene regulation mechanism by which expression of a particular gene can be induced by targeting its promoter using small double‐stranded RNA also known as small activating RNA (saRNA). We used saRNA as a molecular tool to examine NKX3‐1's role as a tumor suppressor and tested in vitro and in vivo antitumor effects of NKX3‐1 induction by saRNA.MATERIALS AND METHODSNKX3‐1 saRNA was transfected into human prostate cancer cells including LNCaP, CWR22R, PC‐3, CWR22RV1, DuPro, LAPC4, and DU145. The transfected cells were used for analysis of gene expression by RT‐PCR and immunoblotting, proliferation, apoptosis and cell cycle distribution. PC‐3 xenograft models were established in immunocompromised mice and treated with NKX3‐1 saRNA.RESULTSNKX3‐1 saRNA induced NKX3‐1 expression in different prostate cancer cell lines, resulting in inhibited cell proliferation and survival, cell cycle arrest and apoptotic cell death. These effects were partly mediated by NKX3‐1's regulation of several downstream genes including the upregulation of p21 and p27, and the inhibition of VEGFC expression. Treatment of mouse xenograft prostate tumors with intratumoral delivery of NKX3‐1 saRNA formulated in lipid nanoparticles significantly inhibited tumor growth and prolonged animal survival.CONCLUSIONSBy revealing several important target genes of NKX3‐1, our findings corroborated NKX3‐1's role as a tumor suppressor gene through direct regulation of the cell cycle and growth/survival pathways. This study also validated the therapeutic potential of saRNA for the treatment of prostate cancer via targeted activation of tumor suppressor genes. Prostate 73: 1591–1601, 2013 © 2013 Wiley Periodicals, Inc.
Measuring Differential Maternal Mortality Using Census Data in Developing Countries
Authors: Leone Tiziana 
Published: July 2013

ABSTRACTThe 2010 census round has highlighted an increasing number of countries that have included maternal mortality in their questionnaires. Censuses have been hailed as a key source of data for maternal mortality in the absence of complete vital registration information. In particular, given the small numbers, they might be the only source of information to estimate differential mortality. This paper explores the feasibility of using census data to analyse differentials (e.g. by education and age) of maternal mortality in low‐resource countries.By using data from Lesotho and Nicaragua, this study investigates the use of censuses to calculate differential maternal mortality. Methods used include indirect demographic techniques, smoothing functions, and sensitivity analysis to analyse maternal mortality by age, residence, and education.Results show that levels of adjustments vary greatly and that smoothing functions, although very useful for differential analysis, might not be powerful enough to avoid fluctuations because of small numbers. Despite the considerable investment over the last decade, results show that the census might not be a feasible tool to analyse differentials as the results suffer greatly from mortality coverage assumptions. Notwithstanding, censuses should still be considered as a key source of information and should be analysed in conjunction with other sources. Copyright © 2013 John Wiley & Sons, Ltd.
Effect of surface roughness in the determination of the mechanical properties of material using nanoindentation test
Authors: Xia Yang , Bigerelle Maxence , Marteau Julie , Mazeran Pierre‐Emmanuel , Bouvier Salima , Iost Alain 
Published: July 2013

SummaryA quantitative model is proposed for the estimation of macro‐hardness using nanoindentation tests. It decreases the effect of errors related to the non‐reproducibility of the nanoindentation test on calculations of macro‐hardness by taking into account the indentation size effect and the surface roughness. The most innovative feature of this model is the simultaneous statistical treatment of all the nanoindentation loading curves. The curve treatment mainly corrects errors in the zero depth determination by correlating their positions through the use of a relative reference. First, the experimental loading curves are described using the Bernhardt law. The fitted curves are then shifted, in order to simultaneously reduce the gaps between them that result from the scatter in the experimental curves. A set of shift depths, Δhc, is therefore identified. The proposed approach is applied to a large set of TiAl6V4 titanium‐based samples with different roughness levels, polished by eleven silicon carbide sandpapers from grit paper 80 to 4,000. The result reveals that the scatter degree of the indentation curves is higher when the surface is rougher. The standard deviation of the shift Δhc is linearly connected to the standard deviation of the surface roughness, if the roughness is high‐pass filtered in the scale of the indenter (15 µm). Using the proposed method, the estimated macro‐hardness for eleven studied TiAl6V4 samples is in the range of 3.5–4.1 GPa, with the smallest deviation around 0.01 GPa, which is more accurate than the one given by the Nanoindentation MTS™ system, which uses an average value (around 4.3 ± 0.5 GPa). Moreover, the calculated Young's modulus of the material is around 136 ± 20 GPa, which is similar to the modulus in literature. SCANNING 36:134–149, 2014. © 2013 Wiley Periodicals, Inc.
Concise review: The Yin and Yang of intestinal (cancer) stem cells and their progenitors
Authors: Stange Daniel E. , Clevers Hans 
Published: July 2013

Abstract
The intestine has developed over the last few years into a prime model system for adult stem cell research. Intestinal cells have an average lifetime of 5 days, moving within this time from the bottom of intestinal crypts to the top of villi. This rapid self-renewal capacity combined with an easy to follow (mostly) unidirectional movement of cells offers an ideal site to conduct adult stem cell research. The delineation of the active pathways in the intestinal epithelium together with the development of molecular techniques to prove stemness laid the grounds for the identification of the intestinal stem cell. In vitro systems and transgenic mouse models broaden our knowledge on the role of the stem cell niche and those cells that reestablish homeostasis after perturbation of the system. These insights expedited also research on the role of normal adult stem cells in cancer initiation and the factors influencing the maintenance of cancer stem cells.
Mechanically activated fyn utilizes mTORC2 to regulate RhoA and adipogenesis in mesenchymal stem cells
Authors: Thompson William R. , Guilluy Christophe , Xie Zhihui , Sen Buer , Brobst Kaitlyn E. , Yen Sherwin S. , Uzer Gunes , Styner Maya , Case Natasha , Burridge Keith , Rubin Janet 
Published: July 2013

Abstract
Mechanical strain provides an anti-adipogenic, pro-osteogenic stimulus to mesenchymal stem cells (MSC) through generating intracellular signals and via cytoskeletal restructuring. Recently, mTORC2 has been shown to be a novel mechanical target critical for the anti-adipogenic signal leading to preservation of β-catenin. As mechanical activation of mTORC2 requires focal adhesions (FAs), we asked whether proximal signaling involved Src and FAK, which are early responders to integrin-FA engagement. Application of mechanical strain to marrow-derived MSCs was unable to activate mTORC2 when Src family kinases were inhibited. Fyn, but not Src, was specifically required for mechanical activation of mTORC2 and was recruited to FAs after strain. Activation of mTORC2 was further diminished following FAK inhibition, and as FAK phosphorylation (Tyr-397) required Fyn activity, provided evidence of Fyn/FAK cooperativity. Inhibition of Fyn also prevented mechanical activation of RhoA as well as mechanically induced actin stress fiber formation. We thus asked whether RhoA activation by strain was dependent on mTORC2 downstream of Fyn. Inhibition of mTORC2 or its downstream substrate, Akt, both prevented mechanical RhoA activation, indicating that Fyn/FAK affects cytoskeletal structure via mTORC2. We then sought to ascertain whether this Fyn-initiated signal pathway modulated MSC lineage decisions. siRNA knockdown of Fyn, but not Src, led to rapid attainment of adipogenic phenotype with significant increases in adipocyte protein 2, peroxisome proliferator-activated receptor gamma, adiponectin, and perilipin. As such, Fyn expression in mdMSCs contributes to basal cytoskeletal architecture and, when associated with FAs, functions as a proximal mechanical effector for environmental signals that influence MSC lineage allocation.
Estimation of shear wave speed in the human uterine cervix
Authors: Carlson L. C. , Feltovich H. , Palmeri M. L. , Dahl J. J. , Munoz del Rio A. , Hall T. J. 
Published: July 2013

ABSTRACTObjectivesTo explore spatial variability within the cervix and the sensitivity of shear wave speed (SWS) to assess softness/stiffness differences in ripened (softened) vs unripened tissue.MethodsWe obtained SWS estimates from hysterectomy specimens (n = 22), a subset of which were ripened (n = 13). Multiple measurements were made longitudinally along the cervical canal on both the anterior and posterior sides of the cervix. Statistical tests of differences in the proximal vs distal, anterior vs posterior and ripened vs unripened cervix were performed with individual two‐sample t‐tests and a linear mixed model.ResultsEstimates of SWS increase monotonically from distal to proximal longitudinally along the cervix, they vary in the anterior compared to the posterior cervix and they are significantly different in ripened vs unripened cervical tissue. Specifically, the mid position SWS estimates for the unripened group were 3.45 ± 0.95 m/s (anterior; mean ± SD) and 3.56 ± 0.92 m/s (posterior), and 2.11 ± 0.45 m/s (anterior) and 2.68 ± 0.57 m/s (posterior) for the ripened group (P < 0.001).ConclusionsWe propose that SWS estimation may be a valuable research and, ultimately, diagnostic tool for objective quantification of cervical stiffness/softness. Copyright © 2013 ISUOG. Published by John Wiley & Sons Ltd.
Turbomole
Authors: Furche Filipp , Ahlrichs Reinhart , Hättig Christof , Klopper Wim , Sierka Marek , Weigend Florian 
Published: July 2013

Turbomole is a highly optimized software package for large‐scale quantum chemical simulations of molecules, clusters, and periodic solids. Turbomole uses Gaussian basis sets and specializes on predictive electronic structure methods with excellent cost to performance characteristics, such as (time‐dependent) density functional theory (TDDFT), second‐order Møller–Plesset theory, and explicitly correlated coupled cluster (CC) methods. These methods are combined with ultraefficient and numerically stable algorithms such as integral‐direct and Laplace transform methods, resolution‐of‐the‐identity, pair natural orbitals, fast multipole, and low‐order scaling techniques. Apart from energies and structures, a variety of optical, electric, and magnetic properties are accessible from analytical energy derivatives for electronic ground and excited states. Recent additions include post‐Kohn–Sham calculations within the random phase approximation, periodic calculations, spin–orbit couplings, explicitly correlated CC singles doubles and perturbative triples methods, CC singles doubles excitation energies, and nonadiabatic molecular dynamics simulations using TDDFT. A dedicated graphical user interface and a user support network are also available.This article is categorized under:

Software > Quantum Chemistry