bluuebunny/crossref_metadata_2025 huggingface dataset:
Portal vein thrombosis and outcomes for pediatric liver transplant candidates and recipients in the United States
Authors: Waits Seth A. , Wojcik Brandon M. , Cai Shijie , Mathur Amit K. , Englesbe Michael J.
Published: July 2011

The effect of occlusive portal vein thrombosis (PVT) on the mortality of pediatric liver transplant candidates and recipients is poorly defined. Using standard multivariate techniques, we studied the relationship between PVT and waiting-list and posttransplant survival rates with data from the Scientific Registry of Transplant Recipients (September 2001 to December 2007). In all, 5087 liver transplant candidates and 3630 liver transplant recipients were evaluated during the period. PVT was found in 1.4% of the liver transplant candidates (n = 70) and in 3.7% of the liver transplant recipients (n = 136). PVT was not associated with increased wait-list mortality [hazard ratio (HR) = 1.1, 95% confidence interval (CI) = 0.5-2.4, P = 0.77]. Conversely, PVT patients had a significantly lower unadjusted survival rate in the posttransplant period (P = 0.01). PVT was independently associated with increased posttransplant mortality in multivariate models (30-day survival: HR = 2.9, 95% CI = 1.6-5.3, P = 0.001; overall survival: HR = 1.7, 95% CI = 1.1-2.4, P = 0.01). The presence of PVT in pediatric liver candidates was not associated with increased wait-list mortality but was clearly associated with posttransplant mortality, especially in the immediate postoperative period. Liver Transpl 17:1066–1072, 2011. © 2011 AASLD.
Singularities of Brill‐Noether loci for vector bundles on a curve
Authors: Casalaina‐Martin Sebastian , Bigas Montserrat Teixidor i
Published: July 2011

In this paper we consider the singularities of the varieties parameterizing stable vector bundles of fixed rank and degree with sections on a smooth curve of genus at least two. In particular, we extend results of Y. Laszlo, and of the second author, regarding the singularities of generalized theta divisors. © 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim
Maternal folate supply and sex influence gene‐specific DNA methylation in the fetal gut
Authors: McKay Jill A. , Wong Yi K. , Relton Caroline L. , Ford Dianne , Mathers John C.
Published: July 2011

Scope: Epidemiological evidence supports the developmental origins of health and disease hypothesis that developmental under/over‐nutrition increases adulthood disease risk. Epigenetic markings are one potential mechanism mediating these effects. Altered folate supply may influence methyl group availability for DNA methylation. We reported low folate supply in utero was associated with reduced global DNA methylation in the murine small intestine of adult offspring. We hypothesised that aberrant methylation would be observed during early development.

Methods and results: Female C57BL/6J mice were fed diets containing 2 mg folic acid/kg or 0.4 mg folic acid/kg 4 wk before mating and during pregnancy. At 17.5 day gestation, gene methylation in fetal gut was analysed by Pyrosequencing®. Low folate reduced overall methylation of Slc394a by 3.4% (p=0.038) but did not affect Esr1 or Igf2 differentially methylated region (DMR) 1. There were sex‐specific differences in Slc394a and Esr1 methylation (2.4% higher in females (p=0.002); 4% higher in males (p=0.0014), respectively).

Conclusion: This is the first study reporting causal effects of maternal folate depletion on gene‐specific methylation in fetal gut. These observations support reports that altered methyl donor intake during development affects DNA methylation in the offspring. The consequences of epigenetic changes for health throughout the life course remain to be investigated.
A double‐Fourier approach to enhance the efficiency of the indirect domain sampling in 2D NMR
Authors: Chandrashekar Srinivasan , Shrot Yoav , Frydman Lucio
Published: July 2011

The relatively long times that may be involved in high‐resolution two‐dimensional nuclear magnetic resonance (2D NMR) have stimulated the search for alternative schemes to collect these data. Particularly onerous situations arise when both high‐resolution and large spectral widths are sought along the indirect domain. Strategies proposed for dealing with such cases include folding‐over procedures, Hadamard encoding, and nonlinear data sampling. This communication discusses an alternative strategy, which exploits a partial prior knowledge regarding the position of the NMR resonances along the indirect domain together with customized excitations for every particular t1 increment, to achieve an optimal sampling in terms of resolution and bandwidth. On the basis of such optimized encoding of the indirect‐domain evolution, which can easily be coped with by modern spectrometers, it becomes possible to maximize the resolution of fine structures without compromising on the spectral bandwidths. The processing of the resulting data along the indirect domain is based on the use of two serially applied discrete Fourier transforms; one to distinguish the main bands in the spectrum and the other to resolve the latter's fine features. A number of simple heteronuclear correlation experiments illustrating the significant acquisition time savings and simultaneous improvements in resolution that can be achieved with the resulting double‐Fourier encoding procedure are illustrated. Copyright © 2011 John Wiley & Sons, Ltd.
Structure elucidation of a sodium salified anthraquinone from the seeds of Cassia obtusifolia by NMR technique assisted with acid–alkali titration
Authors: Zhang Chen , Wang Rufeng , Liu Bin , Tu Guangzhong
Published: July 2011

A new sodium salt of anthraquinone named sodium emodin‐1‐O‐β‐gentiobioside, together with nine known compounds, viz. rubrofusarin‐6‐O‐β‐D‐gentiobioside, chrysophanol‐1‐O‐β‐D‐glucopyranosyl‐(1–3)‐β‐D‐glucopyranosyl‐(1–6)‐β‐D‐glucopyranoside, obtusifolin‐2‐O‐β‐D‐glucopyranoside, aurantio‐obtusin‐6‐O‐β‐D‐glucopyranoside, physcion‐8‐O‐β‐D‐glucopyranoside, 1‐hydroxyl‐2‐acetyl‐3,8‐dimethoxy‐6‐O‐β‐D‐apiofuranosyl‐(1–2)‐β‐D‐glucosylnaphthalene, toralactone‐9‐O‐β‐D‐gentiobioside, aurantio‐obtusin, rubrofusarin‐6‐O‐β‐D‐apiofuranosyl‐(1–6)‐O‐β‐D‐glucopyranoside, was isolated from the seeds of Cassia obtusifolia and its structure was elucidated by 1H and 13C NMR technique assisted with acid–alkali titration. The change of chemical shifts of sodium emodin‐1‐O‐β‐gentiobioside before and after acid–alkali titration was also characterized. Copyright © 2011 John Wiley & Sons, Ltd.
Complete assignment of NMR data of 22 phenyl‐1H‐pyrazoles' derivatives
Authors: de Oliveira Aline Lima , Alves de Oliveira Carlos Henrique , Mairink Laura Maia , Pazini Francine , Menegatti Ricardo , Lião Luciano Morais
Published: July 2011

Complete assignment of 1H and 13C NMR chemical shifts and J(1H/1H and 1H/19F) coupling constants for 22 1‐phenyl‐1H‐pyrazoles' derivates were performed using the concerted application of 1H 1D and 1H, 13C 2D gs‐HSQC and gs‐HMBC experiments. All 1‐phenyl‐1H‐pyrazoles' derivatives were synthesized as described by Finar and co‐workers. The formylated 1‐phenyl‐1H‐pyrazoles' derivatives were performed under Duff's conditions. Copyright © 2011 John Wiley & Sons, Ltd.
Interobserver agreement of medical research council sum‐score and handgrip strength in the intensive care unit
Authors: Hermans Greet , Clerckx Beatrickx , Vanhullebusch Tine , Segers Johan , Vanpee Goele , Robbeets Christophe , Casaer Michael Paul , Wouters Pieter , Gosselink Rik , Van Den Berghe Greet
Published: July 2011

Introduction: Muscle weakness often complicates critical illness and is associated with devastating short‐ and long‐term consequences. For interventional studies, reliable measurements of muscle force in the intensive care unit (ICU) are needed. Methods: To examine interobserver agreement, two observers independently measured Medical Research Council (MRC) sum‐score (n = 75) and handgrip strength (n = 46) in a cross‐sectional ICU sample. Results: The intraclass correlation coefficient (ICC) for MRC sum‐score was 0.95 (0.92–0.97). The kappa coefficient for identifying “significant weakness” (MRC sum‐score <48, MRC subtotal upper limbs <24) and “severe weakness” (MRC sum‐score <36) was 0.68 ± 0.09, 0.88 ± 0.07, and 0.93 ± 0.07, respectively. The ICC for left and right handgrip strength was 0.97 (0.94–0.98) and 0.93 (0.86–0.97), respectively. Conclusions: Interobserver agreement on MRC sum‐score and handgrip strength in the ICU was very good. Agreement on “severe weakness” (MRC sum‐score <36) was excellent and supports its use in interventional studies. Agreement on “significant weakness” (MRC sum‐score <48) was good, but even better using the equivalent cut‐off in the upper limbs. It remains to be determined whether this may serve as a substitute. Muscle Nerve 45: 18–25, 2012
Magnetic resonance imaging of peripheral nerves: Differences in magnetization transfer
Authors: Gambarota Giulio , Krueger Gunnar , Theumann Nicolas , Mekle Ralf
Published: July 2011

Introduction: Magnetic resonance imaging (MRI) is an excellent imaging modality for soft tissues. Magnetization transfer (MT) imaging is an MRI technique that is sensitive to the bound protons of macromolecules and therefore can aid in the assessment of nerve damage.

Methods: Measurements of the MT ratio (MTR), which provides an index of the MT effects in tissues, were performed in the wrist and foot of 5 volunteers.

Results: The MTR of foot (interdigital) nerves (22.2 ± 2.1%) was smaller than that of the median nerve (41.1 ± 1.4%). No difference was observed between MTR in muscles adjacent to foot nerves (46.0 ± 1.5%) and muscles adjacent to the median nerve (44.2 ± 1.9%).

Conclusions: In this study we demonstrate the feasibility of measuring the MTR of foot nerves. The difference of MTR between median and foot nerves indicates a difference in structure/composition. The MTR of peripheral nerves may serve as a biomarker of nerve damage, collagen integrity, and demyelination. Muscle Nerve 45: 13–17, 2012
Downlink fairness‐aware adaptive resource allocation approach for LTE networks
Authors: Ali‐Yahiya Tara , Alagha Khaldoun
Published: July 2011

This article addresses downlink resource allocation strategies in LTE release 8, using orthogonal frequency division access (OFDMA). We consider 3GPP long‐term evolution resource allocation strategies for allocating higher‐layer data to the basic resource allocation units (slots) of OFDMA frames. Then, we introduce two simple allocation methods: adaptive slot allocation and reservation‐based slot allocation. Both approaches consider a fair resource allocation among different types of service data flow (SDF) by considering their quality of service (QoS) characteristics and their channel qualities. The ultimate objective of the proposed approaches is to maximize the capacity of the system subject to the QoS constraints for each type of SDF in terms of data rate and bit error rate. Copyright © 2011 John Wiley & Sons, Ltd.
In situ lineage tracking of human prostatic epithelial stem cell fate reveals a common clonal origin for basal and luminal cells
Authors: Blackwood John K , Williamson Stuart C , Greaves Laura C , Wilson Laura , Rigas Anastasia C , Sandher Raveen , Pickard Robert S , Robson Craig N , Turnbull Douglass M , Taylor Robert W , Heer Rakesh
Published: July 2011

Stem cells accumulate mitochondrial DNA (mtDNA) mutations resulting in an observable respiratory chain defect in their progeny, allowing the mapping of stem cell fate. There is considerable uncertainty in prostate epithelial biology where both basal and luminal stem cells have been described, and in this study the clonal relationships within the human prostate epithelial cell layers were explored by tracing stem cell fate. Fresh‐frozen and formalin‐fixed histologically‐benign prostate samples from 35 patients were studied using sequential cytochrome c oxidase (COX)/succinate dehydrogenase (SDH) enzyme histochemistry and COX subunit I immunofluorescence to identify areas of respiratory chain deficiency; mtDNA mutations were identified by whole mitochondrial genome sequencing of laser‐captured areas. We demonstrated that cells with respiratory chain defects due to somatic mtDNA point mutations were present in prostate epithelia and clonally expand in acini. Lineage tracing revealed distinct patterning of stem cell fate with mtDNA mutations spreading throughout the whole acinus or, more commonly, present as mosaic acinar defects. This suggests that individual acini are typically generated from multiple stem cells, and the presence of whole COX‐deficient acini suggests that a single stem cell can also generate an entire branching acinar subunit of the gland. Significantly, a common clonal origin for basal, luminal and neuroendocrine cells is demonstrated, helping to resolve a key area of debate in human prostate stem cell biology. Copyright © 2011 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Overexpression of the oncostatin M receptor in cervical squamous cell carcinoma cells is associated with a pro‐angiogenic phenotype and increased cell motility and invasiveness
Authors: Winder David M , Chattopadhyay Anasuya , Muralidhar Balaji , Bauer Julien , English William R , Zhang Xiao , Karagavriilidou Konstantina , Roberts Ian , Pett Mark R , Murphy Gillian , Coleman Nicholas
Published: July 2011

Oncostatin M receptor (OSMR) shows frequent copy number gain and overexpression in advanced cervical squamous cell carcinoma (SCC). We used cell‐based in vitro assays, RNA interference, and integrative gene expression profiling to investigate the functional significance of this observation. CaSki and SW756 were selected as representative cervical SCC cells that overexpressed OSMR, and ME180 and MS751 as cells that did not. The STAT‐dependent pro‐angiogenic factors VEGF‐A and ID1 were rapidly induced by OSM in CaSki/SW756 but not in ME180/MS751. However, rapid induction did occur in MS751 following forced OSMR overexpression, while depleting OSMR in CaSki abrogated VEGF‐A expression. Conditioned medium from both CaSki and SW756 stimulated endothelial tube formation in vitro, effects that were inhibited by depleting OSMR in the SCC cells. For both CaSki and SW756, migration in a wound healing assay and invasion through Matrigel were stimulated by OSM and consistently inhibited by OSMR depletion. The phenotype was rescued by transfection with OSMR containing a silent mutation that provided specific siRNA resistance. Overall, there was a positive correlation between OSMR levels and invasiveness. We used gene expression profiling to identify genes induced by OSM in CaSki/SW756 but not in ME180/MS751. The most prominent gene ontology category groups for the differentially expressed genes were cell motility/invasion, angiogenesis, signal transduction, and apoptosis. We also profiled 23 cervical SCC samples, identifying genes that were differentially expressed in cases with OSMR overexpression versus those without. Integration of the datasets identified 15 genes that showed consistent differential expression in association with OSMR levels in vitro and in vivo. We conclude that OSMR overexpression in cervical SCC cells provides increased sensitivity to OSM, which induces pro‐malignant changes. OSMR is a potential prognostic and therapeutic target in cervical SCC. The genes that mediate OSM:OSMR effects will be valuable indicators of the effectiveness of antibody blockade in pre‐clinical systems. Copyright © 2011 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Determination of Natural Pyrethrins by Liquid Chromatography‐Electron Ionisation‐Mass Spectrometry
Authors: Cappiello Achille , Tirillini Bruno , Famiglini Giorgio , Trufelli Helga , Termopoli Veronica , Flender Cornelia
Published: July 2011

Introduction

Pyrethrum extract is a mixture of six insecticidal compounds from the flower heads of Chrysanthemum cinerariaefolium L.. Since they only have low to moderate mammalian toxicity they can be used as natural insecticides in agriculture or to develop low cost and safe dermatological formulations. Because of the thermal instability of pyrethrins, analytical methods based on liquid chromatography (LC) are preferred over those based on gas chromatography (GC). A few applications using LC with mass spectrometry detection are presented in the literature. Current protocols for their characterisation by LC rely on the use of less sophisticated detectors such as UV detection.

Objective

To develop the first liquid chromatography‐electron ionisation‐mass spectrometry (LC‐EI‐MS) method for pyrethrins detection and quantitation in pyrethrum extracts.

Methodology

A commercial pyrethrum extract and various samples of flower heads from C. cinerariaefolium L. were investigated using reversed‐phase nano‐liquid chromatography coupled to direct electron ionisation‐mass spectrometry (nanoLC‐direct EI‐MS). The eluted compounds were identified through searches of the US National Institute of Standards and Technology (NIST) library, exploiting the direct EI capability to produce high quality EI mass spectra.

Results

The method demonstrated satisfactory sensitivity (limit of detection (LOD) range: 0.04–0.38 mg/g), linearity (R2 range: 0.9740–0.9983) and precision (RSD% range: 4–13%) for the quantitation of the natural pyrethrins in extracts from C. cinerariaefolium L.

Conclusion

The nanoLC‐direct EI‐MS technique can be a useful tool for the detection of pyrethrins. Copyright © 2011 John Wiley & Sons, Ltd.
Undoing Descartes: integrating diabetes care for those with mental illness
Authors: Holt RIG
Published: July 2011

Diabetes UK has supported the concept of integrated diabetes care to ensure that the person with diabetes is seen by the right professional at the right time in the right place. At a time when diabetes teams are threatened by changes in the NHS, the division between mental and physical health services makes those with mental illness particularly vulnerable.

The association between diabetes and mental illness has been recognised for over 350 years. The prevalence of diabetes in people with depression and severe mental illness (schizophrenia and bipolar illness) is increased two‐ to three‐fold. Furthermore, the proportion of people with undiagnosed diabetes is considerably higher than in the general population. The risk of complications and diabetes related mortality is higher in those with co‐morbid mental illness.

Currently, diabetes services for people with severe mental illness lag behind those for people without mental illness; patients are less likely to be examined for eye or foot complications, less likely to be screened for glycated haemoglobin or cholesterol, and less likely to receive education.

Integration of care between mental and physical health services, whether in primary or secondary care, is essential if this health inequality is to be overcome. Perhaps only then can we bring body, mind and soul back together. Copyright © 2011 John Wiley & Sons.

This paper was presented as the 2011 Mary MacKinnon lecture at the 2011 Diabetes UK Annual Professional Conference held in London
Phase changes of poly(alkoxyphosphazenes), and their behavior in the presence of oligoisobutylene
Authors: Weikel Arlin L. , Lee David K. , Krogman Nicholas R. , Allcock Harry R.
Published: July 2011

A series of closely related polyphosphazenes with propoxy, pentoxy, hexoxy, octoxy, isostearyloxy, and 2‐(2‐methoxyethoxy)ethoxy (MEE) side groups, together with cosubstituent species with both the alkoxy and MEE side chains, were studied for their morphology and miscibility with oligoisobutylene (OIB). All the pure polymers except one had a single glass transition temperature. The exception was the species with both isostearyloxy and MEE side groups, which underwent two low‐temperature second‐order transitions, even though 31P NMR spectra indicated the absence of a block‐type structure. For the single‐substituent macromolecules, the solubility at 80°C in OIB increased as the length of the unbranched alkoxy side groups rose from propoxy to octoxy (from 1 to 11 wt/wt%). However, the polymer with two isostearyloxy side chains per repeat unit had a low solubility in OIB (3 wt/wt%), and the species with the two MEE side groups on every repeat unit was totally insoluble. When both alkoxy and MEE side groups were present, the solubility in OIB was also low (0–3%), except for the species with both isostearyloxy and MEE side groups, which was soluble in OIB at a level of 21 wt/wt% at 80°C, and showed Tg evidence of polymer/oligomer miscibility even at −80°C. Explanations are suggested for the unusual behavior of this polymer. POLYM. ENG. SCI., 2011. © 2011 Society of Plastics Engineers
Stochastic modeling and simulation of photopolymerization process
Authors: Altun‐Çiftçioğlu Gökçen A. , Ersoy‐Meriçboyu Ayşegül , Henderson Clifford L.
Published: July 2011

In this study, the effect of photoinitiator concentration on the gelation time of different resins were studied in the absence of oxygen in the reaction volume by using passive microrheology technique. Four different monomers which are ethoxylated pentaerythritol tetraacrylate (SR494), trimethylolpropane triacrylate (SR351), triethylene glycol diacrylate (SR272), and 2(2‐ethoxyetoxy) ethyl acrylate (SR256) were used in these experiments. Resins were prepared from these four different monomers by mixing them with various amount of 2,2‐dimethoxy 1,2‐diphenylethanone photoinitiator molecule with high absorption coefficient at the frequency of UV light used in these experiment. The simulations of the results obtained from microrheology experiments were carried out with the new model based on the stochastic Monte Carlo approach in order to account for the inherently random and discrete nature of the photopolymerization reactions. The model captures the nonlinear decrease of gelation time with increasing photoinitator concentration and number of acrylate fragments on each monomer. POLYM. ENG. SCI., 2011. © 2011 Society of Plastics Engineers
Optimization of froth flotation procedure for poly(ethylene terephthalate) recycling industry
Authors: Carvalho M. Teresa , Ferreira Célia , Santos Liliana R. , Paiva M. Conceição
Published: July 2011

This article addresses the separation of polyethylene terephthalate (PET) from ternary blends with polyvinyl chloride (PVC) and polystyrene (PS) by froth flotation. The experimental work was carried out with representative samples from post‐consumer waste packages collected at drop‐off‐points. Previous to froth flotation, PET selective wetting was achieved by alkaline treatment followed by surfactant adsorption. For this purpose, an aqueous solution of NaOH and an industrial detergent commonly used for waste plastic washing were tested as alkaline treatment, and calcium lignosulphonate and Hostaphat were tested as surfactants. An enriched product with 98.9% grade in PET and only 0.6% in PVC was recovered in the nonfloated product. The PET recovery in this product was 97% while ∼96% of PVC and 91% of PS were recovered in the floated product. An analytical method was developed for the quantification of the waste plastic composition. The method was based on the selective dissolution of the plastics in the mixture. POLYM. ENG. SCI., 2012. © 2011 Society of Plastics Engineers
Investigating the role of FGF‐2 in stem cell maintenance by global phosphoproteomics profiling
Authors: Zoumaro‐Djayoon Adja D. , Ding Vanessa , Foong Leong‐Yan , Choo Andre , Heck Albert J. R. , Muñoz Javier
Published: July 2011

Human embryonic stem cells (hESCs) are of immense interest for regenerative medicine as a source of tissue replacement. Expansion of hESCs as a pluripotent population requires a balance between survival, proliferation and self‐renewal signals. One of the key growth factors that maintains this balance is fibroblast growth factor‐2 (FGF‐2). However, the underlying molecular mechanisms are poorly understood. We recently profiled specifically tyrosine phosphorylation events that occur during FGF‐2 stimulation of hESCs (Ding et al., J. Cell. Physiol. 2010, 225, 417–428). Here, we complement this phosphoproteome profiling by analyzing temporal dynamics of mostly serine and threonine protein phosphorylation events. Our multi‐dimensional strategy combines strong cation exchange chromatography to reduce the sample complexity followed by titanium dioxide off‐line for the enrichment of phosphopeptides and dimethylation‐based stable isotope labeling for quantification. This approach allowed us to identify and quantify 3261 unique proteins from which 1064 proteins were found to be phosphorylated in one or more residues (representing 1653 unique phosphopeptides). Approximately 40% of the proteins (553 unique phosphopeptides) showed differential phosphorylation upon FGF‐2 treatment. Among those are several members of the canonical pathways involved in pluripotency and self‐renewal (e.g. Wnt and PI3K/AKT), hESC‐associated proteins such as SOX2, RIF1, SALL4, DPPA4, DNMT3B and 53 proteins that are target genes of the pluripotency transcription factors SOX2, OCT4 and NANOG. These findings complement existing pluripotency analyses and provide new insights into how FGF‐2 assists in maintaining the undifferentiated state of hESCs.
A universally applicable process for preparing stoichiometrically 1:1 labelled functional proteins
Authors: Friedrich Achim , Hoheisel Jörg D. , Knemeyer Jens‐Peter , Marmé Nicole
Published: July 2011

A universally applicable labelling and purification process was established to prepare biologically active proteins with a stoichiometric 1:1 ratio of attached dye‐label. The dye‐label is linked to a specific DNA sequence, which acts as a barcode‐like tag for affinity purification. The DNA‐dye tag is covalently bound to the target protein, which is present in excess to assure the binding of not more than one dye per molecule. Affinity purification occurs at magnetic beads that are functionalized with oligonucleotides that are complementary to the DNA‐tag of the labelled proteins but for one or two mismatches. Washing removes all unbound, unlabelled molecules. The labelled protein is subsequently released by the addition of a fully complementary oligonucleotide. This process allows a gentle purification of a protein fraction that has exactly one label attached to each molecule under conditions that preserve protein structure.
Identification of core–attachment complexes based on maximal frequent patterns in protein–protein interaction networks
Authors: Yu Liang , Gao Lin , Kong ChuiLiang
Published: July 2011

In this paper, we present a method for core–attachment complexes identification based on maximal frequent patterns (CCiMFP) in yeast protein–protein interaction (PPI) networks. First, we detect subgraphs with high degree as candidate protein cores by mining maximal frequent patterns. Then using topological and functional similarities, we combine highly similar protein cores and filter insignificant ones. Finally, the core–attachment complexes are formed by adding attachment proteins to each significant core. We experimentally evaluate the performance of our method CCiMFP on yeast PPI networks. Using gold standard sets of protein complexes, Gene Ontology (GO), and localization annotations, we show that our method gains an improvement over the previous algorithms in terms of precision, recall, and biological significance of the predicted complexes. The colocalization scores of our predicted complex sets are higher than those of two known complex sets. Moreover, our method can detect GO‐enriched complexes with disconnected cores compared with other methods based on the subgraph connectivity.
A Cloud Rise Model for Dust and Soot from High Explosive Detonations
Authors: Cao Xiaoying , Roy Gilles , Brousseau Patrick , Erhardt Lorne , Andrews William
Published: July 2011

Traditionally, the evolution and rise of the dust and soot cloud resulting from high explosive detonations has been divided into two stages, with specific models used for each stage. In this study, based on the assumption that cloud formation progresses smoothly from stage to stage, a simple cloud rise model has been developed based on three sets of field tests of high explosive detonations (25×10−3 to 4.5 kg of detasheet and C‐4). This model provides a good fit to observations and measurements of clouds from detonations both at ground level and 1 m above the ground. It was also found that the detonation height has a noticeable influence on cloud rise before reaching its effective height, but the influence is minor on the subsequent cloud rise.
Applications of High‐Nitrogen Energetics in Pyrotechnics: Development of Perchlorate‐Free Red Star M126A1 Hand‐Held Signal Formulations with Superior Luminous Intensities and Burn Times
Authors: Sabatini Jesse J. , Nagori Amita V. , Latalladi Eric A. , Poret Jay C. , Chen Gary , Damavarapu Reddy , Klapötke Thomas M.
Published: July 2011

Perchlorate‐free hand‐held signal illuminant formulations for the M126A1 red star parachute have been developed. The formulations exhibited longer burn times and higher luminous intensities compared to the US Army in‐service M126A1 formulation. The perchlorate‐free formulations derive their enhanced performance from the inclusion of strontium bis‐(1‐methyl‐5‐nitriminotetrazolate) monohydrate, the choice of magnesium used, and replacing a polyester binder system with an epoxy binder system.
A combinatorial histidine scanning library approach to engineer highly pH‐dependent protein switches
Authors: Murtaugh Megan L. , Fanning Sean W. , Sharma Tressa M. , Terry Alexandra M. , Horn James R.
Published: July 2011

There is growing interest in the development of protein switches, which are proteins whose function, such as binding a target molecule, can be modulated through environmental triggers. Efforts to engineer highly pH sensitive protein–protein interactions typically rely on the rational introduction of ionizable groups in the protein interface. Such experiments are typically time intensive and often sacrifice the protein's affinity at the permissive pH. The underlying thermodynamics of proton‐linkage dictate that the presence of multiple ionizable groups, which undergo a pKachange on protein binding, are necessary to result in highly pH‐dependent binding. To test this hypothesis, a novel combinatorial histidine library was developed where every possible combination of histidine and wild‐type residue is sampled throughout the interface of a model anti‐RNase A single domain VHH antibody. Antibodies were coselected for high‐affinity binding and pH‐sensitivity using anin vitro, dual‐function selection strategy. The resulting antibodies retained near wild‐type affinity yet became highly sensitive to small decreases in pH, drastically decreasing their binding affinity, due to the incorporation of multiple histidine groups. Several trends were observed, such as histidine “hot‐spots,” which will help enhance the development of pH switch proteins as well as increase our understanding of the role of ionizable residues in protein interfaces. Overall, the combinatorial approach is rapid, general, and robust and should be capable of producing highly pH‐sensitive protein affinity reagents for a number of different applications.
Histidine in continuum electrostatics protonation state calculations
Authors: Couch Vernon , Stuchebrukhov Alexei
Published: July 2011

A modification to the standard continuum electrostatics approach to calculate protein pKas, which allows for the decoupling of histidine tautomers within a two‐state model, is presented. Histidine with four intrinsically coupled protonation states cannot be easily incorporated into a two‐state formalism, because the interaction between the two protonatable sites of the imidazole ring is not purely electrostatic. The presented treatment, based on a single approximation of the interrelation between histidine's charge states, allows for a natural separation of the two protonatable sites associated with the imidazole ring as well as the inclusion of all protonation states within the calculation. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Is the prediction of pKavalues by constant‐pH molecular dynamics being hindered by inherited problems?
Authors: Machuqueiro Miguel , Baptista António M.
Published: July 2011

In this study, we investigate two factors that can hinder the performance of constant‐pH molecular dynamics methods in predicting protein pKavalues, using hen egg white lysozyme as a test system. The first factor is related to the molecular definition and pKavalue of model compounds in the Poisson‐Boltzmann framework. We address this by defining the model compound as a molecular fragment with an associated pKavalue that is calibrated against experimental data, which results in a decrease of 0.12 units in pKaerrors. The second addressed factor is the possibility that detrimental structural distortions are being introduced in the simulations by the underlying molecular mechanics force field. This issue is investigated by analyzing how the gradual structural rearrangements affect the predicted pKavalues. The two GROMOS force fields studied here (43A1 and 53A6) yield good pKapredictions, although a time‐dependent performance is observed: 43A1 performs better after a few nanoseconds of structural reorganization (pKaerrors of ∼0.45), while 53A6 gives the best prediction right at the first nanosecond (pKaerrors of 0.42). These results suggest that the good performance of constant‐pH molecular dynamics methods could be further improved if these force field limitations were overcome. Proteins 2011;. © 2011 Wiley‐Liss, Inc.
A new residue‐nucleotide propensity potential with structural information considered for discriminating protein‐RNA docking decoys
Authors: Li Chun Hua , Cao Li Bin , Su Ji Guo , Yang Yong Xiao , Wang Cun Xin
Published: July 2011

Understanding the key factors that influence the preferences of residue‐nucleotide interactions in specific protein‐RNA interactions has remained a research focus. We propose an effective approach to derive residue‐nucleotide propensity potentials through considering both the types of residues and nucleotides, and secondary structure information of proteins and RNAs from the currently largest nonredundant and nonribosomal protein‐RNA interaction database. To test the validity of the potentials, we used them to select near‐native structures from protein‐RNA docking poses. The results show that considering secondary structure information, especially for RNAs, greatly improves the predictive power of pair potentials. The success rate is raised from 50.7 to 65.5% for the top 2000 structures, and the number of cases in which a near‐native structure is ranked in top 50 is increased from 7 to 13 out of 17 cases. Furthermore, the exclusion of ribosomes from the database contributes 8.3% to the success rate. In addition, some very interesting findings follow: (i) the protein secondary structure element π‐helix is strongly associated with RNA‐binding sites; (ii) the nucleotide uracil occurs frequently in the most preferred pairs in which the unpaired and non‐Watson‐Crick paired uracils are predominant, which is probably significant in evolution. The new residue‐nucleotide potentials can be helpful for the progress of protein‐RNA docking methods, and for understanding the mechanisms of protein‐RNA interactions. Proteins 2012; © 2011 Wiley Periodicals, Inc.
Automated tertiary structure prediction with accurate local model quality assessment using the intfold‐ts method
Authors: McGuffin Liam J. , Roche Daniel B.
Published: July 2011

The IntFOLD‐TS method was developed according to the guiding principle that the model quality assessment (QA) would be the most critical stage for our template‐based modeling pipeline. Thus, the IntFOLD‐TS method firstly generates numerous alternate models, using in‐house versions of several different sequence‐structure alignment methods, which are then ranked in terms of global quality using our top performing QA method—ModFOLDclust2. In addition to the predicted global quality scores, the predictions of local errors are also provided in the resulting coordinate files, using scores that represent the predicted deviation of each residue in the model from the equivalent residue in the native structure. The IntFOLD‐TS method was found to generate high quality 3D models for many of the CASP9 targets, whilst also providing highly accurate predictions of their per‐residue errors. This important information may help to make the 3D models that are produced by the IntFOLD‐TS method more useful for guiding future experimental work. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Solution NMR structure of VF0530 from Vibrio fischeri reveals a nucleic acid‐binding function
Authors: Aramini James M. , Rossi Paolo , Fischer Markus , Xiao Rong , Acton Thomas B. , Montelione Gaetano T.
Published: July 2011

Protein domain family PF09905 (DUF2132) is a family of small domains of unknown function that are conserved in a wide range of bacteria. Here we describe the solution NMR structure of the 80‐residue VF0530 protein from Vibrio fischeri, the first structural representative from this protein domain family. We demonstrate that the structure of VF0530 adopts a unique four‐helix motif that shows some similarity to the C‐terminal double‐stranded DNA (dsDNA) binding domain of RecA, as well as other nucleic acid binding domains. Moreover, gel shift binding data indicate a potential dsDNA binding role for VF0530. Proteins 2011; © 2011 Wiley‐Liss, Inc.
MCCE analysis of the pKas of introduced buried acids and bases in staphylococcal nuclease
Authors: Gunner M. R. , Zhu Xuyu , Klein Max C.
Published: July 2011

The pKas of 96 acids and bases introduced into buried sites in the staphylococcal nuclease protein (SNase) were calculated using the multiconformation continuum electrostatics (MCCE) program and the results compared with experimental values. The pKas are obtained by Monte Carlo sampling of coupled side chain protonation and position as a function of pH. The dependence of the results on the protein dielectric constant (ϵprot) in the continuum electrostatics analysis and on the Lennard–Jones non‐electrostatics parameters was evaluated. The pKas of the introduced residues have a clear dependence on ϵprot, whereas native ionizable residues do not. The native residues have electrostatic interactions with other residues in the protein favoring ionization, which are larger than the desolvation penalty favoring the neutral state. Increasing ϵprot scales both terms, which for these residues leads to small changes in pKa. The introduced residues have a larger desolvation penalty and negligible interactions with residues in the protein. For these residues, changing ϵprot has a large influence on the calculated pKa. An ϵprot of 8–10 and a Lennard–Jones scaling of 0.25 is best here. The X‐ray crystal structures of the mutated proteins are found to provide somewhat better results than calculations carried out on mutations made in silico. Initial relaxation of the in silico mutations by Gromacs and extensive side chain rotamer sampling within MCCE can significantly improve the match with experiment. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Optical spectra of nitride quantum‐dot systems: From tight‐binding states to many‐body effects
Authors: Seebeck J. , Lorke M. , Schulz S. , Schuh K. , Gartner P. , Jahnke F.
Published: July 2011

A microscopic theory for optical properties of self‐assembled quantum‐dot systems is presented. For nitride‐based material systems, the single‐particle states are determined from atomistic tight‐binding (TB) calculations. This includes not only localized quantum‐dot states but also delocalized wetting‐layer states, since both contribute to the optical properties and are coupled via interaction processes. The TB wave functions are used to calculate matrix elements for optical dipole transitions as well as Coulomb and LO–phonon interaction of carriers. Absorption and gain spectra are investigated via a solution of the semiconductor Bloch equations including Coulomb interaction effects as well as dephasing due to carrier interaction with LO–phonons. Numerical results are presented for InN/GaN QD‐WL systems and allow to investigate the excitation‐density dependence of the optical spectra for this particular system.
Depth profile characterization of spin‐coated poly(3,4‐ethylenedioxythiophene): poly(styrene sulfonic acid) (PEDOT:PSS) films by spectroscopic ellipsometry
Authors: Ino Tomohisa , Hayashi Tatsuya , Fukuda Takeshi , Ueno Keiji , Shirai Hajime
Published: July 2011

Depth profiles of the optical constants, carrier mobility, and carrier density of spin‐coated poly(3,4‐ethylene‐dioxythiophene):(polystyrene sulfonic acid) (PEDOT:PSS) films were investigated by real‐time spectroscopic ellipsometry (SE) characterization during argon plasma etching at atmospheric pressure. Spectra analysis revealed that homogeneous etching occurred within 10‐20 nm of the top surface, followed by the appearance of conductive PEDOT phase with a surface roughening. These findings originated from the depth profile of the PEDOT‐to‐PSS molar concentration ratio. The use of a 10‐20‐nm etched PEDOT:PSS layer improved relatively the performance of a hole‐transport layer for CuPc/C60 organic thin‐films solar cells with higher optical transmittance (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Large area thin film silicon modules with 10% efficiency for production
Authors: Klein Stefan , Wieder Stephan , Buschbaum Susanne , Rohde Martin , Schwanitz Konrad , Stolley Tobias , Stömmer Christian , Severin Daniel , Straub Axel , Schmidt Ursula I. , Ahmed Khaled
Published: July 2011

A stabilized total‐area efficiency above 10% (ISC = 1.46 A, VOC = 148 V, FF = 67%, Pmpp = 145W, total area of 1.43m2) has been achieved on Gen 5 modules for the first time with an amorphous/microcrystalline silicon solar cell. The efficiency was enhanced by improving the light management and reducing the light induced degradation. The short circuit current density Jsc was enhanced by the introduction of internal light trapping using textured ZnO as the front transparent conductor, the implementation of an innovative µc‐SiOx based p‐layer and by an optical filter between the top and bottom cells of the tandem junction. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Control of a chain of integrators subject to actuator saturation and disturbances
Authors: Wang Xu , Saberi Ali , Stoorvogel Anton A. , Grip Håvard Fjær
Published: July 2011

In this paper, we study control of a chain of integrators under actuator saturation and non‐additive disturbances. We shall show that boundedness of the states can be ensured if the disturbances are matched and integral‐bounded, misaligned and magnitude‐bounded, or a combination of the two, using either a static or a dynamic low‐gain state feedback. This result is an extension of our earlier work on double integrator. Copyright © 2011 John Wiley & Sons, Ltd.
Impulsive consensus of multi‐agent directed networks with nonlinear perturbations
Authors: Xiong Wenjun , Ho Daniel W. C. , Cao Jinde
Published: July 2011

This paper investigates the consensus problem of a multi‐agent directed network with nonlinear perturbations (MNNP). Our main objective is to study how the nonlinear perturbations affect a consensus of a multi‐agent network. Based on a reduced‐order transformation, it is shown that an MNNP cannot reach a consensus under a hypothesis even though the discussed network has a spanning tree. The hypothesis shows a detailed relationship between the nonlinear perturbations and the structure of the multi‐agent network. An impulsive approach is then introduced, and a simple criterion is presented to guarantee the consensus of all agents for an MNNP. Finally, a numerical example is provided to illustrate the effectiveness of the obtained criterion. Copyright © 2011 John Wiley & Sons, Ltd.
A sensitive and selective sensor‐coated molecularly imprinted sol–gel film incorporating β‐cyclodextrin‐multi‐walled carbon nanotubes and cobalt nanoparticles‐chitosan for oxacillin determination
Authors: Hu Yufang , Zhang Zhaohui , Zhang Huabin , Luo Lijuan , Yao Shouzhuo
Published: July 2011

A sensitive and selective imprinted electrochemical sensor for the determination of oxacillin was developed based on indium tin oxide electrode. The proposed sensor was decorated with imprinted sol–gel film and cobalt nanoparticles‐chitosan/β‐cyclodextrin‐multiwalled carbon nanotubes nanocomposites. The surface morphologies of the modified electrodes were characterized by scanning electron microscopy and transmission electron microscope. The stepwise assembly process and electrochemical behavior of the novel sensor were characterized by differential pulse voltammetry, cyclic voltammetry and Amperometric i‐t response. The imprinted sensor displayed excellent selectivity toward oxacillin. Meanwhile, the introduced cobalt nanoparticles‐chitosan and β‐cyclodextrin‐multi‐walled carbon nanotubes exhibited noticeable amplified electrochemical response signal. The differential voltammetric anodic peak current was linear to oxacillin concentration in the range from 2.0 × 10−7 to 1.0 × 10−4 mol·l−1, and the detection limit was 6.9 × 10−9 mol·l−1. The proposed imprinted sensor was applied to the determination of oxacillin in human blood serum samples successfully. Copyright © 2011 John Wiley & Sons, Ltd.
The Adult Mouse Dentate Gyrus Contains Populations of Committed Progenitor Cells that are Distinct from Subependymal Zone Neural Stem Cells
Authors: Clarke Laura , van der Kooy Derek
Published: July 2011

There is currently a debate as to whether or not a neural stem cell (NSC) exists in the adult mammalian hippocampus. Clonal colony-forming assays allow single cells to cells to be evaluated for stem cell properties: self-renewal and multipotentiality. In these in vitro assays, single cells from the subependymal zone (SEZ) of the adult lateral ventricle yield large colonies which self-renew and are multipotential, while single cells from the adult dentate gyrus (DG) produce small, unipotent, and nonself-renewing colonies. We find that multipotential and long-term self-renewing colonies can be isolated only from the early embryonic hippocampus, before the formation of the DG. No movement of progenitors from the postnatal SEZ to the newly forming DG subgranular zone is detected and adult DG colonies in vitro originate from the embryonic hippocampal primordium. These data support a model where embryonic hippocampal NSCs change their properties as the organism ages. When adult DG spheres are cocultured with embryonic brain slices, self-renewal (but not multipotentiality) is restored and maintained for several passages off of slices. Adult clonal DG spheres grown on embryonic brain slices or transplanted into brains of neonatal mice do not give rise to neurons. Neurons arise from separate, small clones that are approximately 10 times more frequent than sphere colonies in vitro and may be responsible for maintaining neurogenesis in the adult in vivo. We propose that there are separate glial and neuronal clones in the adult hippocampus, with glial progenitors being the most proliferative in culture.