bluuebunny/crossref_metadata_2025 huggingface dataset:
Proteomics analyses of microvesicles released byDrosophilaKc167 and S2 cells
Authors: Koppen Tim , Weckmann Andreas , Müller Stefan , Staubach Simon , Bloch Wilhelm , Dohmen R. Jürgen , Schwientek Tilo
Published: September 2011

Distinct types of vesicles are formed in eukaryotic cells that conduct a variable set of functions depending on their origin. One subtype designated circulating microvesicles (MVs) provides a novel form of intercellular communication and recent work suggested the release and uptake of morphogens in vesicles byDrosophilacells. In this study, we have examined cells of the hemocyte‐like cell lines Kc167 and S2 and identified secreted vesicles in the culture supernatant. The vesicles were isolated and found to have characteristics comparable to exosomes and plasma membrane MVs released by mammalian cells. Inwingless‐transfected cells, the full‐length protein was detected in the vesicle isolates. Proteomics analyses of the vesicles identified 269 proteins that include various orthologs of marker proteins and proteins with putative functions in vesicle formation and release. Analogous to their mammalian counterparts, the subcellular origin of the vesicular constituents of both cell lines is dominated by membrane‐associated and cytosolic proteins with functions that are consistent with their localization in MVs. The analyses revealed a significant overlap of the Kc167 and S2 vesicle proteomes and confirmed a close correlation with non‐mammalian and mammalian exosomes.
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

Halophyte, 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

A 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

A 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

Two 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

Aggregation 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

Background

Several 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.

Methods

Eighty‐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).

Results

Ninety‐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.

Conclusions

Although 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

Given 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

Bronchopulmonary 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

Maternal 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

Objectives

We 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 design

Multicenter, 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.

Results

Sixty‐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.

Conclusions

Treatment 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

Background

Chronic 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.

Objective

We sought to determine whether non‐adherence was associated with increased CLDP‐related morbidities and to identify predictors of adherence.

Methods

Recruited 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).

Results

Self‐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).

Conclusions

We 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

VHH 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

Accurate 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.
Confidence Intervals for Process Capability Indices for the Unbalanced One‐Way Random Effect ANOVA Model
Authors: Jose K. K. , Luke Jane A.
Published: September 2011

Confidence intervals for process capability index Cpk are developed for the unbalanced one‐way random effect model using Bissell's approximation method. The proposed limit is compared with the generalized lower confidence limit obtained using the generalized pivotal quantity method. To assess the accuracy of the method, a simulation study is presented. The results are illustrated with an industrial example. Copyright © 2011 John Wiley & Sons, Ltd.
A classification for community discovery methods in complex networks
Authors: Coscia Michele , Giannotti Fosca , Pedreschi Dino
Published: September 2011

Many real‐world networks are intimately organized according to a community structure. Much research effort has been devoted to develop methods and algorithms that can efficiently highlight this hidden structure of a network, yielding a vast literature on what is called todaycommunity detection. Since network representation can be very complex and can contain different variants in the traditional graph model, each algorithm in the literature focuses on some of these properties and establishes, explicitly or implicitly, its own definition of community. According to this definition, each proposed algorithm then extracts the communities, which typically reflect only part of the features of real communities. The aim of this survey is to provide a ‘user manual’ for the community discovery problem. Given a meta definition of what a community in a social network is, our aim is to organize the main categories of community discovery methods based on the definition of community they adopt. Given a desired definition of community and the features of a problem (size of network, direction of edges, multidimensionality, and so on) this review paper is designed to provide a set of approaches that researchers could focus on. The proposed classification of community discovery methods is also useful for putting into perspective the many open directions for further research. © 2011 Wiley Periodicals, Inc. Statistical Analysis and Data Mining 4: 512–546, 2011
Confidence sets for network structure
Authors: Airoldi Edoardo M. , Choi David S. , Wolfe Patrick J.
Published: September 2011

Latent variable models are frequently used to identify structure in dichotomous network data, in part, because they give rise to a Bernoulli product likelihood that is both well understood and consistent with the notion of exchangeable random graphs. In this article, we propose conservative confidence sets that hold with respect to these underlying Bernoulli parameters as a function of any given partition of network nodes, enabling us to assess estimates of residual network structure, that is, structure that cannot be explained by known covariates and thus cannot be easily verified by manual inspection. We demonstrate the proposed methodology by analyzing student friendship networks from the National Longitudinal Survey of Adolescent Health that include race, gender, and school year as covariates. We employ a stochastic expectation‐maximization algorithm to fit a logistic regression model that includes these explanatory variables as well as a latent stochastic blockmodel component and additional node‐specific effects. Although maximum‐likelihood estimates do not appear consistent in this context, we are able to evaluate confidence sets as a function of different blockmodel partitions, which enables us to qualitatively assess the significance of estimated residual network structure relative to a baseline, which models covariates but lacks block structure. © 2011 Wiley Periodicals, Inc. Statistical Analysis and Data Mining 4: 461–469, 2011
Combining a Nanowire SERRS Sensor and a Target Recycling Reaction for Ultrasensitive and Multiplex Identification of Pathogenic Fungi
Authors: Yoo Seung Min , Kang Taejoon , Kang Hyungchang , Lee Hyoban , Kang Mijeong , Lee Sang Yup , Kim Bongsoo
Published: September 2011

Development of a rapid, sensitive, and multiplex pathogen DNA sensor enables early diagnosis and, subsequently, the proper treatment of infectious diseases, increasing the possibility to save the lives of infected patients. Here, the development of an ultrasensitive and multiplex pathogen DNA detection method that combines a patterned Au nanowire (NW)‐on‐film surface‐enhanced resonance Raman scattering (SERRS) sensor with an exonuclease III‐assisted target DNA recycling reaction is reported. Multiple probe DNAs are added to the target DNA solution, and among them, only the complementary probe DNA is selectively digested by exonuclease III, resulting in the decrease in its concentration. The digestion process is repeated by recycling of target DNAs. The decrease of the complementary probe DNA concentration is detected by SERRS. Combining the high sensitivity of the NW‐on‐film sensor and the target recycling reaction significantly improves DNA detection performance, resulting in the detection limit of 100 fM corresponding to 3 amole. By positioning Au NWs at specific addresses, multiple pathogen DNAs can be identified in a single step. Clinical sample tests with multiple genomic DNAs of pathogens show the potential of this sensor for practical diagnosis of infectious diseases.
Evaluation of system reliability for a cloud computing system with imperfect nodes
Authors: Lin Yi‐Kuei , Chang Ping‐Chen
Published: September 2011

From the perspective of system design and quality of service (QoS), system reliability is one of the essential performance indicators to measure the probable reliability of a network. In terms of a practical cloud computing system (CCS), edges and nodes have various capacities or states due to failure, partial failure, or maintenance. Thus, the CCS is a typical capacitated‐flow network. To guarantee a good level of quality and reliability, the CCS should be maintained, so as not to fall into a failed state whereby it cannot provide sufficient capacity to satisfy demand. Thus, system reliability is developed in this paper to evaluate the capability of the CCS to send d units of data from the cloud to the client through two paths under both the maintenance budget and time constraints. An algorithm with an adjusting procedure based on the branch‐and‐bound approach is proposed to evaluate the system reliability. The relevant proof shows that the proposed algorithm is reasonable and appropriate for measuring the system reliability of the CCS. According to different maintenance budgets and corresponding system reliability, the system supervisor could determine a reasonable maintenance budget to maintain a good level of quality and reliability of the CCS. From the perspective of system design, the system supervisor could further conduct a sensitivity analysis to improve or investigate the most important part in a large CCS based on system reliability. © 2011 Wiley Periodicals, Inc.
Increased Aortic Stiffness Can Predict Perioperative Cardiovascular Outcomes in Patients Undergoing Noncardiac, Nonvascular Surgery
Authors: Biteker Murat , Duman Dursun , Dayan Akın , İlhan Erkan
Published: September 2011

Background

Aortic stiffness is an early marker of arteriosclerosis and associated with cardiovascular mortality. However, the impact of aortic stiffness on perioperative cardiovascular outcomes in patients undergoing noncardiac surgery is unknown.

Methods

The study population was composed of 660 consecutive adults aged 18 years and over (mean age = 65.3 ± 14 years) who underwent intermediate‐risk (nonvascular), noncardiac surgery between January 2010 and February 2011. Nonemergency, non‐day‐case, open surgical procedures were enrolled. Aortic stiffness indices were calculated from the aortic diameters measured by echocardiography. Electrocardiography and cardiac biomarkers were evaluated 1 day before surgery, and on days 1, 3, and 7 after surgery.

Results

Eighty patients (12.1%) experienced perioperative cardiovascular events (PCE). Preoperative aortic distensibility (AD) (2 ± 1.3 vs. 2.9 ± 1.1 cm2/dyn/103, P < 0.001) and aortic strain (AS) (4.4 ± 2.4 vs. 6.4 ± 1.9, P < 0.001) of the patients with PCE were significantly lower than in patients without PCE. Univariate analysis showed a significant association between age, diabetes mellitus (DM), coronary artery disease, preoperative atrial fibrillation, American Society of Anesthesiologists (ASA) status, Revised Cardiac Risk Index, left ventricle ejection fraction (LVEF), AD, aortic strain, and in‐hospital PCE. However, on multivariate logistic regression analysis, only AD (OR: 1.94, 95% CI: 1.1–3.4; P = 0.02), AS (OR: 0.45, 95% CI: 0.3–0.6; P < 0.001), DM (OR: 2.28, 95% CI: 1.08–4.82; P = 0.03), and LVEF (OR: 0.96, 95% CI: 0.93–0.99; P = 0.03) remained as significant variables associated with PCE.

Conclusion

Impaired elastic properties of the aorta are associated with increased PCE rates in patients undergoing noncardiac, nonvascular surgery.
Electrospray Ionization Tandem Mass Spectrometry of Sodiated Adducts of Cholesteryl Esters
Authors: Bowden John A. , Shao Fei , Albert Carolyn J. , Lally John W. , Brown Robert J. , Procknow Jesse D. , Stephenson Alan H. , Ford David A.
Published: September 2011

Cholesteryl esters (CE) are important lipid storage molecules. The present study demonstrates that sodiated adducts of CE molecular species form positive ions that can be detected in both survey scan mode as well as by exploiting class‐specific fragmentation in MS/MS scan modes. A common neutral loss for CE is the loss of cholestane (NL 368.5), which can be used to specifically quantify tissue CE molecular species. Using this MS/MS technique, CE molecular species were quantified in mouse monocyte‐derived macrophages (J774 cells) incubated with either linoleic (18:2) or arachidonic acid (20:4). These studies revealed that arachidonic acid was not only incorporated into the CE pool, but also was elongated resulting in the accumulation of 22:4 and 24:4 CE molecular species in macrophages. Additionally, this technique was used to quantify CE molecular species present in crude lipid extracts from plasma of female mice fed a Western diet, which led to an enrichment in CE molecular species containing monounsaturated fatty acids compared to female mice fed a normal chow diet. Last, NL 368.5 spectra revealed the oxidation of the aliphatic fatty acid residues of CE molecular species containing polyunsaturated fatty acids. Taken together, these studies demonstrate the utility of using sodiated adducts of CE in conjunction with direct infusion electrospray ionization tandem mass spectrometry to rapidly quantify CE molecular species in biological samples.
The Influence of Growing Region on Fatty Acids and Sterol Composition of Iranian Olive Oils by Unsupervised Clustering Methods
Authors: Piravi‐Vanak Z. , Ghasemi Jahan B. , Ghavami M. , Ezzatpanah H. , Zolfonoun E.
Published: September 2011

Twenty seven Iranian olive oil samples were collected from different provinces to evaluate fatty acids and sterol compositions. The samples were collected from different geographical locations that varied in altitude, temperature, humidity and rain fall. The sample collected from the northern part of Iran by the Caspian Sea had higher oleic acid [G2 sample (75.98%)] and lower linoleic acid [Go5 sample (6.5%)] and palmitic acid [G2 sample (10.78%)] concentrations than samples from the southern part of the country such as F1 whose contents of C16:0, C18:1 and C18:2 were 15.27, 62.73 and 16.09%, respectively, in the southern part, the climate is dry and the temperature variation is wider and the elevation is 1,488 m. The results indicated that oleic acid was the predominant fatty acid with 62.7% for F1 sample in the warmer climate at the south of Iran to 76.0% for G2 sample in the cooler climate in the north of Iran. According to the results, the highest content of β‐sitosterol was 87% related to samples G9 and Z3 from the north of Iran and the lowest content was 69.95% related to sample F1–24 from the south of Iran. Clustering techniques such as principal component analysis and hierarchical cluster analysis were carried out on olive composition data to show similarities and discrimination between samples as a function of the cultivation zone. The two methods applied clearly showed the effect of growing regions on the distribution of the olive oil samples in the high dimensional space created by fatty acid and sterol compositions.
Ethiopia's assessment of emergency obstetric and newborn care: Setting the gold standard for national facility‐based assessments
Authors: Keyes Emily B. , Haile‐Mariam Abonesh , Belayneh Neghist T. , Gobezie Wasihun A. , Pearson Luwei , Abdullah Muna , Kebede Henok
Published: September 2011

Objective

To describe the methods used to implement Ethiopia's 2008 emergency obstetric and newborn care services (EmONC) assessment; highlight how the collaborative process contributed to immediate integration of results into national and subnational planning; and explain how the experience informed the development of a set of tools providing best practices and guidelines for other countries conducting similar assessments.

Methods

A team of maternal and newborn health experts from the Federal Ministry of Health (FMOH), the United Nations Children's Fund (UNICEF), the World Health Organization (WHO), and the United Nations Population Fund (UNFPA), together with representatives from the Ethiopian Society of Obstetricians and Gynecologists, provided technical guidance for the 18‐month process and facilitated demand for and use of the assessment results. Eighty‐four trained data collectors administered 9 data collection modules in 806 public and private facilities. Field work and data were managed by a private firm who, together with the core team, implemented a multi‐layered plan for data quality. Columbia University's Averting Maternal Death and Disability Program provided technical assistance.

Results

Results were published in national and regional reports and in 1‐page facility factsheets informing subnational planning activities. Assessment results—which have been published in journal articles—informed water infrastructure improvements, efforts to expand access to magnesium sulfate, and FMOH and UN planning documents. The assessment also established a permanent database for future monitoring of the health system, including geographic locations of surveyed facilities.

Conclusion

Ethiopia's assessment was successful largely because of active local leadership, a collaborative process, ample financial and technical support, and rapid integration of results into health system planning.
Indicators for availability, utilization, and quality of emergency obstetric care in Ethiopia, 2008
Authors: Admasu Keseteberhan , Haile‐Mariam Abonesh , Bailey Patricia
Published: September 2011

Objective

To report on the availability and quality of emergency obstetric and newborn care (EmONC) in Ethiopia.

Methods

All licensed hospitals and health centers were visited and standard questionnaires were administered. In addition, a nonrandom systematic sample was taken of recent cesarean deliveries, partographs, and maternal deaths—and these cases were systematically reviewed. Health facilities were geocoded using geographic positioning system devices.

Results

Too few facilities provided EmONC to meet the UN standards of 5 per 500 000 population, both nationally and in all but 2 regions. Only 7% of deliveries took place in institutions of any type, and only 3% in facilities that routinely provided all the signal functions. Only 6% of women with obstetric complications were treated in any health facility, half of whom were treated in fully functional EmONC facilities. Nationwide, 0.6% of expected deliveries were by cesarean. The mortality rate for women with serious obstetric complications (case fatality rate) was 2%. The cause of death was unknown in 10% of cases, and 21% were due to indirect causes (primarily malaria, anemia, and HIV‐related).

Conclusion

None of the indicators met UN standards. Ethiopia faces many challenges—not least geography—with regard to improving EmONC. Nevertheless, the government places high priority on improvement and has taken (and will continue to take) action to achieve Millennium Development Goals 4 and 5. This comprehensive survey serves both as a road map for planning strategies for improvement and as a baseline for measuring the impact of interventions.
Late glacial and holocene landscapes of central Beringia
Authors: Lozhkin Anatoly V. , Anderson Patricia , Eisner Wendy R. , Solomatkina Tatiana B.
Published: September 2011

New palynological and sedimentological data from St. Lawrence Island present a rare view into late-glacial and Holocene environments of the central Bering Land Bridge. The late glaciation was a time of dynamic landscape changes in south-central Beringia, with active thermokarst processes, including the formation and drainage of thaw lakes. The presence of such a wet, unstable substrate, if widespread, probably would have had an adverse impact on food sources and mobility for many of the large mammal populations. The establishment ofBetulashrub tundra on the island suggests late-glacial summers that were warmer than present, consistent with regional paleoclimatic interpretations. However, the increasing proximity to the Bering Sea, as postglacial sea levels rose, modified the intensity of warming and prevented the establishment of deciduous forest as found in other areas of Beringia at this time. The mid- to late Holocene is marked by more stable land surfaces and development ofSphagnumand Cyperaceae peat deposits. The accumulation of organic deposits, decline of shrubBetula, and decrease in thermokarst disturbance suggest that conditions were cooler than the previous. A recent decline in peat accumulation at the study sites may relate to local geomorphology, but similar decreases have been noted for other arctic regions.
Formation of rhythmic sorted bed forms on the continental shelf: an idealised model
Authors: Van Oyen Tomas , de Swart Huib , Blondeaux Paolo
Published: September 2011

An idealised model is presented to study the formation of sorted bed forms generated by a wind-driven along-shore current. The study employs a linear stability analysis to describe the time development of perturbations of both bottom composition and bed elevation, superimposed on a flat bed composed of a sediment mixture homogeneously distributed in space. The model considers both bed and suspended loads and takes into account the averaged influence of waves on the flow field and the transport of sediment. The results show that the positive coupling between waves, along-shore current and the erodible heterogeneous bed leads to the amplification of two modes, which exhibit distinct characteristics. A first mode is found to be dominant when moderate hydrodynamic conditions are considered and is primarily amplified by the convergence of sediment transport induced by the changes in the bed elevation. This mode has wavelengths of the order of hundred metres and has coarse (fine) sediments in its troughs (crests). By increasing the height of the waves and/or the strength of the steady current, the second mode can become dominant. This mode is characterised by shorter wavelengths and results from the interaction between the convergence of sediment transport related to changes in the bottom composition and that induced by perturbations of the bed elevation. These bed features can have an up-current or a down-current shift between the centre of the coarse-grained bands and the trough of the bottom wave. Typical growth times of the amplified features are of the order of hundreds of days and the migration rates, in the direction of the along-shore current, range between 0.1 and 10 m per day. A qualitative comparison of the model results with field observations indicates that the generation of two distinct modes provides a possible explanation for the broad range of characteristics of the natural bed features.
GENERALIZED IMPLICIT INCLUSION PROBLEMS ON NONCOMPACT SETS WITH APPLICATIONS
Authors: WANG SAN-HUA , HUANG NAN-JING
Published: September 2011

In this paper, a class of generalized implicit inclusion problems is introduced, which can be regarded as a generalization of variational inequality problems, equilibrium problems, optimization problems and inclusion problems. Some existence results of solutions for such problems are obtained on noncompact subsets of Hausdorff topological vector spaces using the famous FKKM theorem. As applications, some existence results for vector equilibrium problems and vector variational inequalities on noncompact sets of Hausdorff topological vector spaces are given.
ANALYSIS OF FACTORS THAT DETERMINE TEA PRODUCTIVITY IN NORTHEASTERN INDIA: A COMBINED STATISTICAL AND MODELLING APPROACH
Authors: DUTTA RISHIRAJ , SMALING ERIC M. A. , BHAGAT RAJIV MOHAN , TOLPEKIN VALENTYNE A. , STEIN ALFRED
Published: September 2011

This study analyses the factors affecting tea productivity in Northeast India using a combined statistical and modelling approach. The effects of a number of genotypic, environmental and management factors on tea yield are quantified and modelled, using a three-year (2007–2009) field trial in Assam, Northeast India. Simulations of the potential tea yield are obtained using the Cranfield University Plantation Productivity Analysis (CUPPA) Tea model to find out how well the predicted and observed values for tea production match. This combined approach shows that plantation age has a significant negative (R2 = 0.77) effect on tea yield. Monthly rainfall had a significant positive effect on monthly yields (R2 = 0.43). Rainfall was more strongly associated with tea yield when rainfall in month x was related to the tea yield in month x + 1 (R2 = 0.49). When repeating the analysis for a hypothetical situation that the fields are fully planted, the correlation between monthly rainfall in month x and tea yield for month x + 1 increases (R2 = 0.58). Adjusted yields show a higher correlation than actual yields. The results obtained show a close correspondence between predicted and observed yields, indicating that the model could be used on contrasting soil types, genotypes and also on daily, weekly and monthly weather data. It can be further calibrated and validated for Northeast Indian conditions if more required input parameters are collected in a series of plantations. Tea research might benefit from developing new versions of the CUPPA Tea model for the major clonal tea cultivars, with a more flexible module for fertiliser application as is currently the case.