bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coordination of carbon fixation and nitrogen metabolism in Salicornia europaea under salinity: Comparative proteomic analysis on chloroplast proteins
Authors: Fan Pengxiang , Feng Juanjuan , Jiang Ping , Chen Xianyang , Bao Hexigeduleng , Nie Lingling , Jiang Dan , Lv Sulian , Kuang Tingyun , Li Yinxin 
Published: September 2011

AbstractHalophyte, like Salicornia europaea, could make full use of marginal saline land for carbon fixation. How the photosynthesis of S. europaea is regulated under high salinity implicates a significant aspect to exploit this pioneer plant in future. Measurement of photosynthesis parameters demonstrated the reduction of photosynthesis for the 0 and 800 mM NaCl treated plants are more likely due to non‐stomatal limitation, which might be caused by changes in the enzymes associated with photosynthesis. Different salinity induced ultrastructure changes other than photosynthetic apparatus damage, suggesting the photosynthesis of S. europaea might be affected via biochemical regulation. Comparative proteomics analysis of chloroplast proteins by 2‐D gel electrophoresis reproducibly detected 90 differentially expressed proteins, among which 66 proteins were identified by nanoLC MS/MS. Further study of thylakoid membrane proteins by Blue‐Native PAGE proved the increase in abundance of light reaction proteins under salinity. Analysis of gene expression patterns of 12 selected proteins provides evidence for the correlations between transcription and proteomics data. Based on our results, a putative model of photosynthesis regulatory network figured out proper coordination of carbon fixation and nitrogen metabolism in chloroplast of S. europaea under salinity, which provided subcellular level insight into salt tolerance mechanism in S. europaea.
Synthesis and properties of a deuterated phenolic resin
Authors: Izumi Atsushi , Nakao Toshio , Shibayama Mitsuhiro 
Published: September 2011

AbstractA highly deuterated novolac‐type phenolic resin was prepared by polycondensation of deuterated phenol and formaldehyde using oxalic acid as an acid catalyst. The polycondensation of deuterated monomers and the formation of the highly deuterated phenolic resin were confirmed by the gel permeation chromatography, IR, and 1H NMR analyses. With the exception of hydroxyl groups, the degree of deuteration was estimated to be more than 98%. The polymer conformation in THF solution was evaluated by the scaling exponent of the Mark–Houwink–Sakurada equation. The exponent of the deuterated phenolic resin is 0.26 in THF at 40 °C and is close to that of a nondeuterated phenolic resin, which suggests that phenolic resins behave like a compact sphere irrespective of deuteration. The curing behavior of the deuterated phenolic resin with hexamethylenetetramine was confirmed by differential scanning calorimetry analysis. The cured highly deuterated phenolic resin exhibits a lower incoherent neutron scattering background than that of the nondeuterated phenolic resin, which suggests that the former is suitable for matrix resins with low incoherent backgrounds for small‐angle neutron scattering studies of thermosetting resins. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011.
Synthesis and characterization of graft polymethacrylates containing conducting diphenyldithiophene for organic thin‐film transistors
Authors: Hu Zhaokang , Fu Boyi , Aiyar Avishek , Reichmanis Elsa 
Published: September 2011

AbstractA class of [5,5′]‐diphenyl‐[5,5′]‐dithiophene (PTTP)‐modified methacrylates has been synthesized and free radically polymerized to form graft polymethacrylates with the conducting PTTP segments as pendant side chains. Both the terminal alkyl side chain and spacer between the PTTP segments and polymer backbone could be varied to study fundamental structure–property relationships for this class of materials. Specifically, a group of three different PTTP graft polymethacrylates has been successfully synthesized with the alkyl side chain varying from hexyl to dodecyl. For the dodecyl‐terminated poly(4‐(5′‐(4‐dodecylphenyl)‐[2,2′‐bithiophen]‐5‐yl)phenethyl methacrylate), p(DPTTPEM), a counterpart, poly(4‐(5′‐(4‐dodecylphenyl)‐[2,2′‐bithiophen]‐5‐yl)phenbutyl methacrylate), p(DPTTPBM), where the ethyl spacer was replaced by a butyl group, was synthesized. The experimental results indicated that both the alkyl side chain and spacer significantly affected the reactivity of the PTTP‐modified methacrylates during free radical polymerization as well as the physical properties of the resultant graft polymers including solubility, morphology, and electrochemical and electrical properties. Typical field‐effect mobilities on the order of 10−5 cm2 V−1 s−1 were observed for all the PTTP monomers in air, which was attributed to their crystalline phase as revealed by differential scanning calorimetry and X‐ray diffraction studies. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012
Synthesis and polymerizations of six aminophosphonate‐containing methacrylates
Authors: Bilgici Zeynep Sarayli , Ordu Oznur Demir , Isik Mehtap , Avci Duygu 
Published: September 2011

AbstractTwo different groups of novel aminophosphonate‐containing methacrylates were synthesized. The route to the first group involves reactions of ethyl α‐bromomethacryate (EBBr) and t‐butyl α‐bromomethacryate (TBBr) with diethyl aminomethylphosphonate and diethyl 2‐aminoethylphosphonate. Bulk and solution polymerizations at 60–80 °C with 2,2′‐azobis(isobutyronitrile) (AIBN) gave crosslinked or soluble polymers depending on monomer structure and polymerization conditions. Increasing bulkiness from ethyl to t‐butyl decreases the polymerization rate, correlated well with the chemical shift differences of double bond carbons and consistent with the lower molecular weights of t‐butyl ester polymers (Mn = 1800–7900 vs. 50,000–72,000). The route to the second group involves the Michael addition reaction between diethyl aminomethylphosphonate and diethyl 2‐aminoethylphosphonate with 3‐(acryloyloxy)‐2‐hydroxypropyl methacrylate (AHM) to give secondary amines. The photopolymerization using differential scanning calorimeter showed that these monomers have similar or higher reactivities than AHM, even though AHM has two double bonds. The high rates of polymerization of these monomers were attributed to both hydrogen bonding interactions due to additional NH groups as well as chain transfer reactions. All the homopolymers obtained produced char (17–35%) on combustion. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011.
Aggregation behavior of amphiphilic random copolymer of 2‐(acrylamido)‐2‐methylpropanesulfonic acid and tris(trimethylsiloxy)silylpropylmethacrylate in aqueous solution
Authors: Ogata Yoichi , Iwano Munetaka , Mogi Takeshi , Makita Yutaka 
Published: September 2011

AbstractAggregation behavior including dilute solution property and surface‐activity of the amphiphilic random copolymer composed of 2‐(acrylamido)‐2‐methylpropanesulfonic acid and tris(trimethylsiloxy)silylpropylmethacrylate (AMPS/TRIS copolymer) in aqueous solution were studied by static light scattering (SLS), dynamic light scattering (DLS), surface tension measurement, and transmission electron microscopy (TEM). The surface tension measurement made it clear that AMPS/TRIS copolymer exhibited weaker surface‐activity than a typical low‐molecular weight surfactant sodium dodecyl sulfate in water, that is, there were no plateau of surface tension γ versus concentration and no critical micelle concentration (CMC) in the whole concentration studied. SLS and DLS analyses, and TEM revealed that AMPS/TRIS copolymer self‐associated into imperfect core‐shell micelles having hydrophobic TRIS core surrounded by hydrophilic AMPS shell in water. AMPS shell was considered as a hard shell due to the stiffness of AMPS chain in water. TRIS chain could not densely aggregate in water due to the large steric hindrance between bulky trimethylsiloxy groups despite its hydrophobic nature, thereby providing TRIS core with less‐dense structure. The balance between the spreading force of stiff AMPS chain and the cohesion force of bulky TRIS chain provides the driving force for forming the unique micelle having less‐dense TRIS core and hard AMPS shell. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011
Oral contraceptive use in women at increased risk of breast/ovarian cancer: knowledge and attitudes
Authors: Bui Kim Tam , Wakefield Claire E. , Kasparian Nadine A. , Tyler Janet , Abbott Jason , Tucker Kathy 
Published: September 2011

AbstractBackgroundSeveral of the health benefits and risks associated with the combined oral contraceptive pill (COCP) are particularly relevant to women at risk of hereditary breast and/or ovarian cancer.MethodsEighty‐three past female patients of an Australian hereditary cancer clinic aged 18–50 years completed a self‐report questionnaire to assess their contraceptive practices, knowledge and information needs (44% response rate).ResultsNinety‐two percent of participants had previously used the COCP, with a mean knowledge score of 3.63 out of 8. Nearly 40% reported that their family history of cancer was one reason they discontinued/avoided using the COCP. Women reported receiving insufficient COCP information and preferred a targeted information leaflet to answer their questions.ConclusionsAlthough recall bias may have affected some women, there is a clear need to improve the consistency of information delivered to women at risk of hereditary breast and/or ovarian cancer, to ensure informed contraceptive choices are made. Copyright © 2011 John Wiley & Sons, Ltd.
Fifty years of pediatric asthma in developed countries: How reliable are the basic data sources?
Authors: Chawla Jasneek , Seear Michael , Zhang Tingting , Smith Anne , Carleton Bruce 
Published: September 2011

AbstractGiven the difficulties in diagnosing, or even defining, asthma in children, claims of a pediatric asthma epidemic in Canada and other developed countries are accepted with surprisingly little critical examination. We reviewed a broad range of data sources to understand how the epidemic evolved during the last 50 years and also to assess the reliability of the conclusions drawn from that data. We obtained Canadian National and Provincial data from Statistics Canada National Population Health Survey, and the British Columbia Ministry of Health respiratory database. International data were obtained by extensive review of pediatric asthma epidemiological surveys published during the last 50 years. In many developed countries, there have been three separate epidemics involving different aspects of pediatric asthma during the last 50 years: a double peaked mortality epidemic (1960s and 1980s), a hospital admission epidemic (peaked around 1990) and a steadily growing epidemic of children who report asthmatic symptoms on questionnaires. Canadian pediatric rates for asthma mortality (1–2/million/year) and hospital admission (1–2/thousand/year) are low and have fallen for the last 20 years. Rates based on questionnaire studies are high (10–15/hundred) and rose steadily over the same period. Objective reductions in asthma deaths and hospital admission likely reflect improved education and treatment programmes. Current claims of an epidemic based largely on subjective self‐reported symptoms require more careful analysis. The possibility that symptom misperception, disease fashions, and poor recall, may be part of the explanation for the current high levels of self‐reported symptoms deserves more attention. Pediatr Pulmonol. 2012; 47:211–219. © 2011 Wiley Periodicals, Inc.
Hyperoxia arrests alveolar development through suppression of histone deacetylases in neonatal rats
Authors: Zhu Lüchang , Li Huiping , Tang Jun , Zhu Jianxing , Zhang Yongjun 
Published: September 2011

AbstractBronchopulmonary dysplasia (BPD) poses a significant global health problem. It mainly occurs in preterm infants. It is histopathologically characterized by fewer and larger alveoli and less secondary septa, suggesting an arrested or disordered lung development. To date, the mechanisms that lead to the pathophysiological changes in BPD have still not been totally understood. In embryonic development, histone deacetylase (HDAC) plays an important role by regulating gene transcription. Here, we hypothesize that a decreased HDAC expression and activity, caused by preterm birth or environmental stresses, contribute to a disorder in alveolar development in BPD. To this end, newborn Sprague–Dawley rats subjected to hyperoxia (85% O2) were used to investigate the gene expression and protein activity of HDAC and alveolar development in lungs. Our results showed that hyperoxia exposure led to a suppression of the HDAC1/HDAC2 expression and activity, and the overall HDAC activity, as well as arrest of alveolarization, and an elevated expression of the cytokine‐induced neutrophil chemoattractant‐1 (CINC‐1) in the lungs of newborn rats. However, preservation of HDAC activity by theophylline significantly improved alveolar development and attenuated CINC‐1 release, all of which were blocked by a specific HDAC inhibitor, trichostatin A (TSA). TSA alone can disturb the alveolar development in neonatal rats. Our findings indicate that a persistent exposure to hyperoxia leads to a suppressed HDAC activity, which causes disorders in pulmonary development. This effect may be mediated by CINC‐1. Attenuation of CINC‐1‐mediated inflammation by activating HDAC may have a protective effect in BPD. Pediatr Pulmonol. 2012; 47:264–274. © 2011 Wiley Periodicals, Inc.
Fetal hyperglycemia alters lung structural development in neonatal rat
Authors: Koskinen Anna , Lukkarinen Heikki , Moritz Niko , Aho Heikki , Kääpä Pekka , Soukka Hanna 
Published: September 2011

AbstractMaternal diabetes is associated with increased risk for abnormal fetal organogenesis, but its effects on the developing lungs are still insufficiently known. To determine the effect of maternal hyperglycemia on postnatal lung development, we studied lung structural and cellular changes in newborn rats exposed to intrauterine hyperglycemia. We induced hyperglycemia in Sprague–Dawley rats with i.p. streptozotocin before pregnancy and allowed the hyperglycemic and control dams deliver at term. Lungs were obtained on postnatal day (d) 0, d7, and d14 and analyzed for lung weight and morphology, as well as cellular apoptosis (TUNEL staining) and proliferation (PCNA staining). Quantitative micro‐CT analysis of the lung vasculature was additionally performed at d14. At birth, maternal hyperglycemia resulted in decreased relative lung weight, thinner alveolar septa and increased cellular apoptosis and proliferation, when compared to controls. At 1 and 2 weeks of age pulmonary cell apoptosis and alveolar chord length remained unchanged, but cell proliferation and number of secondary crests were increased in the hyperglycemia‐exposed neonatal lungs in comparison with the controls. Density of small arterioles on histological examination and the structure of pulmonary arterial vasculature in micro‐CT analysis of the neonatal lungs were not influenced by maternal hyperglycemia. Our results suggest, that maternal hyperglycemia is related to developmental structural alterations in postnatal rat lungs. These early changes may reflect aberrant maturational adaptation in response to the hyperglycemic fetal environment. Pediatr Pulmonol. 2012; 47:275–282. © 2011 Wiley Periodicals, Inc.
A multi‐center controlled trial of growth hormone treatment in children with cystic fibrosis
Authors: Stalvey Michael S. , Anbar Ran D. , Konstan Michael W. , Jacobs Joan R. , Bakker Bert , Lippe Barbara , Geller David E. 
Published: September 2011

AbstractObjectivesWe evaluated safety and efficacy of recombinant human growth hormone (rhGH) for improving growth, lean body mass (LBM), pulmonary function, and exercise tolerance in children with cystic fibrosis (CF) and growth restriction.Study designMulticenter, open‐label, controlled clinical trial comparing outcomes in prepubertal children <14 years with CF, randomized in a 1:1 ratio to receive daily rhGH (Nutropin AQ) or no treatment (control) for 12 months, followed by a 6‐month observation (month 18). Safety was monitored at each visit, including assessments of glucose tolerance.ResultsSixty‐eight subjects were randomized (control n = 32; rhGH n = 36). Mean height standard deviation score (SDS) in the rhGH group increased by 0.5 ± 0.4 at 12 months (mean ± SD, P < 0.001); the control group height SDS remained unchanged. Weight increased by 3.8 ± 1.8 versus 2.8 ± 1.5 kg, (mean ± SD, P = 0.0356) and LBM increased by 3.8 ± 1.8 versus 2.1 ± 1.4 kg (P = 0.0002) in the rhGH group versus controls, respectively. Forced vital capacity increased by 325 ± 319 in the rhGH group compared with 178 ± 152 ml in controls (mean ± SD, P = 0.032). Forced expiratory volume in 1 sec improved in both groups with a significant difference between groups after adjustment for baseline severity (LS mean ± SE: rhGH, 224 ± 37, vs. controls, 108 ± 40 ml; P = 0.04). There was no difference between groups in exercise tolerance (6‐min walk distance) at 1 year. Changes in glucose tolerance for the two groups were similar over the 12‐month study period, with three subjects developing IGT and one CFRD in each group. One rhGH‐treated patient developed increased intracranial pressure.ConclusionsTreatment with rhGH in prepubertal children with CF was effective in promoting growth, weight, LBM, lung volume, and lung flows, and had an acceptable safety profile. Pediatr Pulmonol. 2012; 47:252–263. © 2011 Wiley Periodicals, Inc.
Respiratory medication adherence in chronic lung disease of prematurity
Authors: Collaco J. Michael , Kole Amanda J. , Riekert Kristin A. , Eakin Michelle N. , Okelo Sande O. , McGrath‐Morrow Sharon A. 
Published: September 2011

AbstractBackgroundChronic lung disease of prematurity (CLDP) is a frequent complication of premature birth. Infants and children with CLDP are often prescribed complex medication regimens, which can be difficult for families to manage.ObjectiveWe sought to determine whether non‐adherence was associated with increased CLDP‐related morbidities and to identify predictors of adherence.MethodsRecruited caregivers of 194 children with CLDP completed questionnaires regarding self‐reported adherence, respiratory outcomes, and quality of life (January 2008–June 2010). Adherence data were available for 176 subjects, of whom 143 had self‐reported data only, and 33 had prescription claims data, which were used to calculate a medication possession ratio (MPR). Participants in the Prescription Claims Sample (n = 33) were more likely to have public insurance (P < 0.001).ResultsSelf‐reported adherence substantially overestimated medication possession; the mean MPR was 38.8% (n = 33) and was not associated with self‐reported adherence (P = 0.71; n = 26). In a small sample, higher MPR was associated with decreased odds ratios of visiting the emergency department (ED) (OR = 0.75 for a 10% increase in MPR [95%CI: 0.58, 0.97]; P = 0.03; n = 74 questionnaires from 28 participants), activity limitations (OR = 0.71 [95%CI: 0.53, 0.95]; P = 0.02; n = 70 questionnaires from 28 participants), and rescue medication use (OR = 0.84 [95%CI: 0.73‐0.98]; P = 0.03; n = 70 questionnaires from 28 participants). Increasing caregiver worries regarding medication efficacy and side effects were associated with lower MPR (P = 0.04 and 0.02, respectively; n = 62 questionnaires from 27 participants). Socio‐demographic and clinical risk factors were not predictors of MPR (n = 33).ConclusionsWe found that non‐adherence with respiratory medications was common in premature infants and children with CLDP. Using multiple timepoints in a small sample, non‐adherence was associated with a higher likelihood of respiratory morbidities. Although self‐reported adherence and demographic characteristics did not predict MPR, concerns about medications did. We suggest that addressing caregiver concerns about medications may improve adherence and ultimately decrease CLDP‐related morbidities. Larger, prospective studies are needed to confirm these findings and determine which factors predict non‐adherence. Pediatr Pulmonol. 2012; 47:283–291. © 2011 Wiley Periodicals, Inc.
Affinity transfer to a human protein by CDR3 grafting of camelid VHH
Authors: Inoue Hidetoshi , IIhara Akiko , Takahashi Hideo , Shimada Ichio , Ishida Isao , Maeda Yoshitake 
Published: September 2011

AbstractVHH is the binding domain of the IgG heavy chain. Some VHHs have an extremely long CDR3 that contributes to antigen binding. We studied the antigen binding ability of CDR3 by grafting a CDR3 from an antigen‐binding VHH onto a nonbinding VHH. cAb‐CA05‐(1RI8), the CDR3‐grafted VHH, had an antigen‐binding ability. To find a human scaffold protein acceptable for VHH CDR3 grafting, we focused on the conserved structure of VHH, especially the N‐terminal and C‐terminal amino acid residues of the CDR3 loop and the Cys residue of CDR1. Human origin protein structures with the same orientation were searched in PDB and ubiquitin was selected. Ubi‐(1RI8), the CDR3‐grafted ubiquitin, had antigen‐binding ability, though the affinity was relatively low compared to cAb‐CA05‐(1RI8). The thermodynamic parameters of Ubi‐(1RI8) binding to HEWL were different from cAb‐CA05‐(1RI8). Hydrogen‐deuterium exchange experiments showed decreased stability around the CDR3 grafting region of Ubi‐(1RI8), which might explain the decreased antigen‐binding ability and the differences in thermodynamic properties. We concluded that the orientation of the CDR3 sequence of Ubi‐(1RI8) could not be reconstructed correctly.
SIDEpro: A novel machine learning approach for the fast and accurate prediction of side‐chain conformations
Authors: Nagata Ken , Randall Arlo , Baldi Pierre 
Published: September 2011

AbstractAccurate protein side‐chain conformation prediction is crucial for protein modeling and existing methods for the task are widely used; however, faster and more accurate methods are still required. Here we present a new machine learning approach to the problem where an energy function for each rotamer in a structure is computed additively over pairs of contacting atoms. A family of 156 neural networks indexed by amino acid and contacting atom types is used to compute these rotamer energies as a function of atomic contact distances. Although direct energy targets are not available for training, the neural networks can still be optimized by converting the energies to probabilities and optimizing these probabilities using Markov Chain Monte Carlo methods. The resulting predictor SIDEpro makes predictions by initially setting the rotamer probabilities for each residue from a backbone‐dependent rotamer library, then iteratively updating these probabilities using the trained neural networks. After convergences of the probabilities, the side‐chains are set to the highest probability rotamer. Finally, a post processing clash reduction step is applied to the models. SIDEpro represents a significant improvement in speed and a modest, but statistically significant, improvement in accuracy when compared with the state‐of‐the‐art for rapid side‐chain prediction method SCWRL4 on the following datasets: (1) 379 protein test set of SCWRL4; (2) 94 proteins from CASP9; (3) a set of seven large protein‐only complexes; and (4) a ribosome with and without the RNA. Using the SCWRL4 test set, SIDEpro's accuracy (χ1 86.14%, χ1+2 74.15%) is slightly better than SCWRL4‐FRM (χ1 85.43%, χ1+2 73.47%) and it is 7.0 times faster. On the same test set SIDEpro is clearly more accurate than SCWRL4‐rigid rotamer model (RRM) (χ1 84.15%, χ1+2 71.24%) and 2.4 times faster. Evaluation on the additional test sets yield similar accuracy results with SIDEpro being slightly more accurate than SCWRL4‐flexible rotamer model (FRM) and clearly more accurate than SCWRL4‐RRM; however, the gap in CPU time is much more significant when the methods are applied to large protein complexes. SIDEpro is part of the SCRATCH suite of predictors and available from: http://scratch.proteomics.ics.uci.edu/. Proteins 2012; © 2011 Wiley Periodicals, Inc.