bluuebunny/crossref_metadata_2025 huggingface dataset:
Joint modelling of longitudinal and time‐to‐event data with application to predicting abdominal aortic aneurysm growth and rupture
Authors: Sweeting Michael J. , Thompson Simon G.
Published: August 2011

Shared random effects joint models are becoming increasingly popular for investigating the relationship between longitudinal and time‐to‐event data. Although appealing, such complex models are computationally intensive, and quick, approximate methods may provide a reasonable alternative. In this paper, we first compare the shared random effects model with two approximate approaches: a naïve proportional hazards model with time‐dependent covariate and a two‐stage joint model, which uses plug‐in estimates of the fitted values from a longitudinal analysis as covariates in a survival model. We show that the approximate approaches should be avoided since they can severely underestimate any association between the current underlying longitudinal value and the event hazard. We present classical and Bayesian implementations of the shared random effects model and highlight the advantages of the latter for making predictions. We then apply the models described to a study of abdominal aortic aneurysms (AAA) to investigate the association between AAA diameter and the hazard of AAA rupture. Out‐of‐sample predictions of future AAA growth and hazard of rupture are derived from Bayesian posterior predictive distributions, which are easily calculated within an MCMC framework. Finally, using a multivariate survival sub‐model we show that underlying diameter rather than the rate of growth is the most important predictor of AAA rupture.
The Diiodine Basicity Scale: Toward a General Halogen‐Bond Basicity Scale
Authors: Laurence Christian , Graton Jérôme , Berthelot Michel , El Ghomari Mohamed J.
Published: August 2011

The new diiodine basicity scale pKBI2 is quasi‐orthogonal to most known Lewis basicity scales (hydrogen‐bond, dative‐bond and cation basicity scales). The diiodine basicity falls in the sequence N>P≈Se>S>I≈O>Br>Cl>F for the iodine‐bond acceptor atomic site and SbO≈NO≈AsO>SeO>PO>SO>CO>O>SO2 or PS≫S>CS≫NCS for the functionality of oxygen or sulfur bases. Substituent effects are quantified through linear free energy relationships, which allow the calculation of individual complexation constants for each site of polybases and thus the classification of aromatic ethers as carbon π bases and of aromatic amines, thioethers and selenoethers as N, S and Se bases, respectively. The pKBI2 values of nBu3N+‐N−C≡N, 2‐aminopyridine and 1,10‐phenanthroline reveal a superbasic nitrile, a hydrogen‐bond‐assisted iodine bond and a two‐centre iodine bond, respectively. The diiodine basicity scale is a general inorganic but family‐dependent organic halogen‐bond basicity scale because organic halogen‐bond donors such as IC≡N and ICF3 have a stronger electrostatic character than I2. The family independence can be restored by the addition of an electrostatic parameter, either the experimental pKBHX hydrogen‐bond basicity scale or the computed minimum electrostatic potential.
Influence of Moisture Content on the Compression Behavior of Granules
Authors: Müller Peter , Antonyuk Sergiy , Tomas Jürgen
Published: August 2011

Das Materialverhalten von γ‐Al2O3‐, Zeolith 4A‐ und Natriumbenzoatgranulaten bei Druckbeanspruchung wurde experimentell als dominant elastisch, elastisch‐plastisch und dominant plastisch bestimmt. Der Einfluss der Feuchtebeladung auf das Materialverhalten wurde ebenfalls ermittelt. Zudem wurden die Kraft/Weg‐Kurven mit bekannten mechanischen Modellen aus der Literatur approximiert.
Elimination of autoreactive B cells in humanized SCID mouse model of SLE
Authors: Kerekov Nikola S. , Mihaylova Nikolina M. , Grozdev Ivan , Todorov Todor A. , Nikolova Milena , Baleva Marta , Nikolova Maria , Prechl Jozsef , Erdei Anna , Tchorbanov Andrey I.
Published: August 2011

Although the exact etiology of systemic lupus erythematosus (SLE) remains elusive, B‐cell hyperactivity and production of autoantibodies directed to components of the cell nucleus are a well‐established pathogenetic mechanism of the disease. Therefore, the targeted inhibition of DNA‐specific B cells is a logical therapeutic approach. The complement receptor type 1 (CR1, CD35) has been shown to suppress human B‐cell activation and proliferation after co‐cross‐linking with the BCR, and may serve as a mediator for negative signal delivery. In order to evaluate this therapeutic approach in a human‐like system, we used immune‐restricted SCID mice transferred with PBMCs from SLE patients. The tolerance of these humanized SCID mice to native DNA was re‐established after administration of a chimeric molecule consisting of a CR1‐specific mAb coupled to the decapeptide DWEYSVWLSN that mimics dsDNA. The generated protein‐engineered chimera was able to co‐cross‐link selectively native DNA‐specific BCR with the B‐cell inhibitory receptor CR1, thus delivering a strong inhibitory signal.
Water‐Soluble Cobalt(II) and Copper(II) Complexes of 3‐(5‐Chloro‐2‐hydroxy‐3‐sulfophenylhydrazo)pentane‐2,4‐dione as Building Blocks for 3D Supramolecular Networks and Catalysts for TEMPO‐Mediated Aerobic Oxidation of Benzylic Alcohols
Authors: Kopylovich Maximilian N. , Mahmudov Kamran T. , Haukka Matti , Figiel Paweł J. , Mizar Archana , da Silva José A. L. , Pombeiro Armando J. L.
Published: August 2011

A new water‐soluble β‐diketone azo derivative ― 3‐(5‐chloro‐2‐hydroxy‐3‐sulfophenylhydrazo)pentane‐2,4‐dione(H3L, 1) ― was synthesized and found to be stable in DMSO solution and in the solid state in the hydrazo tautomeric form. Its water‐soluble complexes [Co(HL)(en)(H2O)]·4H2O (3) and the zwitterionic [Cu(L)(Hen)(H2O)] (4), with buffering properties, were prepared by reaction of cobalt(II) and copper(II) nitrates with the ethylenediammonium (H2en) salt of 1, (H2en)(HL) (2). In the formation of 3 and 4, 1 is a chelating ligand, and a crucial synthetic and structural role is played by en, allowing the organization of water‐soluble assemblies and influencing the overall 3D supramolecular arrangement. Compound 3 is the first cobalt complex with an azo derivative of a β‐diketone. Complex 4 acts as catalyst precursor for the aerobic TEMPO‐mediated selective oxidation of benzylic alcohols to the corresponding aldehydes in aqueous media.
Cytospolides A–E, New Nonanolides from an Endophytic Fungus, Cytospora sp.
Authors: Lu Shan , Kurtán Tibor , Yang Genjin , Sun Peng , Mándi Attila , Krohn Karsten , Draeger Siegfried , Schulz Barbara , Yi Yanghua , Li Ling , Zhang Wen
Published: August 2011

Cytospolides A–E (1–5), five new nonanolides with an unprecedented 15‐carbon skeleton with the unique chemical feature of a C‐2 methyl group, were isolated from the endophytic fungus Cytospora sp. The structures were elucidated by spectroscopic analysis, chemical interconversion, and single‐crystal XRD. The solution and solid state conformers were compared by experimental methods (X‐ray, NMR) and solvent and gas phase DFT calculations. The absolute configurations were assigned by time dependent (TD)‐DFT calculations of CD spectra, including solution and solid state CD/TD‐DFT approaches. The cytotoxicity assay of C‐2 epimers showed significantly different activity against A549, suggesting that the C‐2 methyl group has an important role in growth inhibition towards the tumor line. The existence of two conformers of the bioactive epimer in solution was proven by the soft pulse transfer NMR technique and further supported by DFT calculations. The discovery of the new metabolites not only extends the nonanolide family with cytospolide‐type skeletons but also gives insight into the biosynthetic process of these fungal metabolites.
Versatile Synthesis of Isoquinolines and Isochromenes by Pd‐Catalyzed Oxidative Carbonylation of (2‐Alkynyl)benzylideneamine Derivatives
Authors: Gabriele Bartolo , Veltri Lucia , Maltese Vito , Spina Rosella , Mancuso Raffaella , Salerno Giuseppe
Published: August 2011

Isoquinoline‐4‐carboxylic esters 3 and isochromene‐4‐carboxylic esters 4 have been conveniently prepared by direct PdI2‐catalyzed oxidative heterocyclization/alkoxycarbonylation of readily available (2‐alkynylbenzylidene)amine derivatives. In particular, (2‐alkynylbenzylidene)(tert‐butyl)amines 2 selectively afforded isoquinoline derivatives 3 by N‐cyclization, whereas N‐(2‐alkynylbenzylidene)‐N′‐phenylhydrazines 5 led to the formation of isochromenes 4 through O‐cyclization ensuing from water attack on the imino group of the substrate. Reactions were carried out in alcoholic solvents at 80–100 °C and under 20–80 atm (at 25 °C) of a 4:1 mixture of CO/air, in the presence of PdI2 (2–10 mol‐%) in conjunction with KI (KI/PdI2 molar ratio = 10). In the case of imines 2, the use of a dehydration agent, such as trialkyl orthoformate, was necessary to obtain satisfactory yields of isoquinolines 3.
Retrospective Maternal Report of Early Eating Behaviours in Anorexia Nervosa
Authors: Dellava Jocilyn E. , Trace Sara E. , Strober Michael , Thornton Laura M. , Klump Kelly L. , Brandt Harry , Crawford Steve , Fichter Manfred M. , Halmi Katherine A. , Johnson Craig , Kaplan Allan S. , Mitchell James E. , Treasure Janet , Woodside D. Blake , Berrettini Wade H. , Kaye Walter H. , Bulik Cynthia M.
Published: August 2011

This exploratory study assessed whether maternal recall of childhood feeding and eating practices differed across anorexia nervosa (AN) subtypes. Participants were 325 women from the Genetics of Anorexia Nervosa study whose mothers completed a childhood feeding and eating questionnaire. Multinomial logistic regression analyses were used to predict AN subtype from measures related to childhood eating: (i) infant feeding (breastfed, feeding schedule, age of solid food introduction), (ii) childhood picky eating (picky eating before age 1 year and between ages one and five) and (iii) infant gastrointestinal problems (vomiting and colic). Results revealed no significant differences in retrospective maternal report of childhood feeding and eating practices among AN subtypes. Copyright © 2011 John Wiley & Sons, Ltd and Eating Disorders Association.
Cost‐effectiveness of memantine in moderate and severe Alzheimer's disease in Norway
Authors: Rive B. , Aarsland D. , Grishchenko M. , Cochran J. , Lamure M. , Toumi M.
Published: August 2011

Background

The cost‐effectiveness of memantine for the treatment of moderate and severe Alzheimer's disease has been assessed in several European countries. Objective of the study was to assess it in Norwegian settings.

Methods

This cost‐utility analysis used a Markov modelling approach to simulate the evolution of patients until their need for full‐time care (FTC) over a 5‐year period. FTC was defined as a patient becoming either dependent or institutionalised. Transition probabilities were estimated using a newly developed predictive equation of time to FTC. Health resource use and utilities were obtained from the Scandinavian Study of Cost and Quality of Life in Alzheimer's Disease study, and mortality was obtained from the Oslo study. Memantine efficacy was based on a meta‐analysis of six large trials. The model compared memantine with its alternative in this population, that is no pharmacological treatment or background therapy with acetylcholinesterase inhibitors. The model underwent extensive sensitivity analyses.

Results

In Norway, memantine was found to delay the need for FTC by 4.4 weeks compared with standard care and was associated with increased quality‐adjusted life years. Memantine was the dominant strategy with cost savings of €3739 (30 041 NOK) per patient. The probability of being the dominant strategy was 98.8%. This result was confirmed across multiple sensitivity analyses.

Conclusions

The model suggests that memantine prolongs time to FTC for no additional cost to the healthcare system and society. It can be regarded as a cost‐effective choice in the management of moderate and severe Alzheimer's disease. Copyright © 2011 John Wiley & Sons, Ltd.
The association of bone density and calcified atherosclerosis is stronger in women without dyslipidemia: The multi-ethnic study of atherosclerosis
Authors: Jensky Nicole E , Hyder Joseph A , Allison Matthew A , Wong Nathan , Aboyans Victor , Blumenthal Roger S , Schreiner Pamela , Carr J Jeffrey , Wassel Christina L , Ix Joachim H , Criqui Michael H
Published: August 2011

We tested whether the association between bone mineral density (BMD) and coronary artery calcification (CAC) varies according to dyslipidemia in community-living individuals. Between 2002 and 2005, 305 women and 631 men (mean age of 64 years), who were not taking lipid-lowering medications or estrogen were assessed for spine BMD, CAC, and total (TC), HDL- and LDL-cholesterol and triglycerides. Participants were a random sample from the Multi-Ethnic Study of Atherosclerosis (MESA) without clinical cardiovascular disease. Spine BMD at the L3 vertebrate was performed by computer tomography (CT). CAC prevalence was measured by CT. The total cholesterol to HDL ratio (TC:HDL) ≥ 5.0 was used as the primary marker of hyperlipidemia. The association of BMD with CAC differed in women with TC:HDL < 5.0 versus higher (p-interaction = 0.01). In age- and race-adjusted models, among women with TC:HDL < 5.0, each SD (43.4 mg/cc) greater BMD was associated with a 25% lower prevalence of CAC (prevalence ratio [PR] 0.75, 95% confidence interval [CI] 0.63–0.89), whereas among women with higher TC:HDL, higher BMD was not significantly associated with CAC (PR 1.22, 95% CI 0.82–1.82). Results were similar using other definitions of hyperlipidemia. In contrast, no consistent association was observed between BMD and CAC in men, irrespective of the TC:HDL ratio (p interaction 0.54). The inverse association of BMD with CAC is stronger in women without dyslipidemia. These data argue against the hypothesis that dyslipidemia is the key factor responsible for the inverse association of BMD with atherosclerosis. © 2011 American Society for Bone and Mineral Research
Medication reconciliation: Barriers and facilitators from the perspectives of resident physicians and pharmacists
Authors: Boockvar Kenneth S. , Santos Susan L. , Kushniruk Andre , Johnson Christopher , Nebeker Jonathan R.
Published: August 2011

BACKGROUND:

Medication reconciliation can prevent medication errors and harm when patients transition between hospital and other care settings. Though a Joint Commission hospital Patient Safety Goal since 2006, organizations continue to have difficulty implementing the process.

OBJECTIVE:

To determine factors that influence performance of medication reconciliation in a hospital setting with a computerized medication reconciliation tool.

DESIGN:

Cognitive task analysis (CTA) and focus group interviews.

SETTING:

Urban, academic, tertiary‐care Veterans Affairs medical center.

PARTICIPANTS:

Internal medicine house staff physicians (n = 23) and inpatient staff pharmacists (n = 12).

MEASUREMENTS:

CTA participants verbalized their thoughts while they completed medication reconciliation with the computerized tool. Focus group participants described medication reconciliation's purpose and effectiveness, how they completed the task, and its barriers and facilitators. Interviews were recorded and analyzed using social science methods for analyzing qualitative data.

RESULTS:

Participants agreed that a central goal of medication reconciliation is to prevent prescribing errors, but disagreed about whether it achieves this goal. Computerization facilitated the task, but participants said that computers and patients can be unreliable sources of information. Participants varied in how they sequenced components of the task. When time was limited, physicians considered other responsibilities higher priority. Both physicians and pharmacists expressed low self‐efficacy, ie, low perceived capability to achieve the objectives of the process.

CONCLUSION:

Key barriers to medication reconciliation are unreliable sources of medication information and tasks that compete for providers' time and attention that they consider higher priority. Addressing these barriers while increasing providers' self‐efficacy might improve medication reconciliation and its outcomes. Journal of Hospital Medicine 2011;6:329–337. © 2011 Society of Hospital Medicine
Evaluation of a hospitalist‐run acute care for the elderly service
Authors: Wald Heidi L. , Glasheen Jeffrey J. , Guerrasio Jeannette , Youngwerth Jean M. , Cumbler Ethan Ulysses
Published: August 2011

BACKGROUND:

Comprehensive care for frail older inpatients may improve selected outcomes and reduce harm.

OBJECTIVE:

To evaluate a Hospitalist‐run Acute Care for the Elderly (Hospitalist‐ACE) service.

DESIGN:

Quasi‐randomized, controlled trial.

SETTING:

Urban academic medical center.

PATIENTS:

Medical inpatients age ≥70 years.

INTERVENTION:

Hospitalist‐ACE service components: 1) selected hospitalist attendings; 2) daily interdisciplinary rounds; 3) standardized geriatric assessment; 4) clinical focus on mitigating harm and discharge planning; 5) novel inpatient geriatrics curriculum.

MEASURES:

The primary outcome was recognition of abnormal functional status by the primary medical team. Secondary outcomes included: recognition of abnormal cognitive status and delirium by the primary medical team; use of physical restraints and sleep aids; documentation of code status; hospital charges, length of stay, readmission rates, discharge location, and falls.

RESULTS:

One hundred twenty‐two Hospitalist‐ACE patients were compared to 95 usual care patients. Hospitalist‐ACE patients had significantly greater recognition of abnormal functional status (65% vs 32%, P < 0.0001), and abnormal cognitive status (57% vs 36%, P = 0.02), and greater use of “Do Not Attempt Resuscitation” orders (39% vs 26%, P = 0.04). There were no differences in use of physical restraints, or sleep aids, falls, or discharge location. Hospitalist‐ACE patients and usual care patients had similar mean lengths of stay in days (3.4 ± 2.7 vs 3.1 ± 2.7, P = 0.52), mean charges ($24,617 ± $15,828 vs $21,488 ± $13,407, P = 0.12), and 30‐day readmission rates (12% vs 10%, P = 0.50).

CONCLUSIONS:

A Hospitalist‐ACE service may improve care processes without significantly increasing resource consumption. No impact on key clinical outcomes was observed. Journal of Hospital Medicine 2011;6:313–321. © 2011 Society of Hospital Medicine
Clinical and safety impact of an inpatient Pharmacist‐Directed anticoagulation service
Authors: Schillig Jessica , Kaatz Scott , Hudson Michael , Krol Gregory D. , Szandzik Edward G. , Kalus James S.
Published: August 2011

BACKGROUND:

Warfarin is implicated in approximately 30% of reported anticoagulant‐related errors. In order to improve anticoagulation management and safety, our institution implemented an inpatient Pharmacist‐Directed Anticoagulation Service (PDAS).

OBJECTIVE:

To evaluate the impact of this service on both transition of care and safety of patients receiving warfarin anticoagulation.

DESIGN:

Cluster randomized trial.

SETTING:

Large, urban teaching hospital and level 1 trauma center.

PATIENTS:

All patients receiving warfarin on two medical and two cardiology units.

INTERVENTION:

A PDAS provided dosing, monitoring, and coordination of transition from the inpatient‐to‐outpatient setting.

MEASUREMENTS:

Endpoints were assessed during hospitalization and 30 days after discharge. Transition of care was considered effective if compliance with all of the transition of care metrics occurred. The transition of care metrics included: appropriate enrollment in the anticoagulation clinic, documented inpatient‐to‐outpatient provider contact, documented inpatient provider‐to‐anticoagulation clinic communication and patient follow‐up with the anticoagulation clinic within five days of discharge. Safety was measured by the composite endpoint of thromboembolism, major bleeding, or international normalized ratio (INR) ≥5.

RESULTS:

This study included 500 patients. Transition of care metric compliance occurred in 73% more patients in the PDAS group (P < 0.001). There was also a 32% reduction in the composite safety endpoint in the PDAS group (P = 0.103). This finding was driven by a reduction in rate of INR ≥5 (P = 0.076).

CONCLUSIONS:

Implementation of a PDAS provides a net improvement in quality of care for the patient taking warfarin in the inpatient setting. Journal of Hospital Medicine 2011;6:322–328. © 2011 Society of Hospital Medicine
CONTENDING DEVELOPMENTS: LOCAL NOTIONS OF DEVELOPMENT ON SIQUIJOR ISLAND, PHILIPPINES
Authors: Bulloch Hannah
Published: August 2011

Post‐development theorists have reminded us that ‘development’ is a cultural construct—a set of organising assumptions through which we order the world and understand our place in it. As such, notions of development are not singular but vary between different groups of people. This paper seeks to bring further nuance to these understandings. Drawing on ethnographic fieldwork on Siquijor Island in the Philippines, it explores contending ideals of the good life—one based on material accumulation, the other on austerity—at once valued by most residents. It shows that notions of development vary not only between groups but that individuals can simultaneously hold multiple ideals of development. Copyright © 2011 John Wiley & Sons, Ltd.
The effect of alternative sweeteners on batter rheology and cake properties
Authors: Psimouli Vasso , Oreopoulou Vassiliki
Published: August 2011

BACKGROUND: The aim of this research was to investigate whether certain polyols (mannitol, maltitol, sorbitol, lactitol), fructose, oligofructose and polydextrose can replace sugar (by an equal amount of each substitute) in cake formulations. The rheological behaviour of the cake batter and the physical characteristics of the cakes containing sugar substitutes were compared with the respective attributes of the control cake. Differential scanning calorimetry was used to investigate the effect of sugar substitutes on starch gelatinisation. Furthermore sensorial characteristics were evaluated by instrumental measurements and sensory evaluation. The correlation of the batter characteristics with the textural attributes of the final product was also attempted.

RESULTS: The best results were obtained by using oligofructose, lactitol or maltitol as sugar replacers, which exhibited similar behaviour to sucrose in terms of batter rheology and increased starch gelatinisation temperature. Fructose and mannitol led to cakes of poor quality characteristics, as was demonstrated by instrumental measurements and sensory evaluation.

CONCLUSIONS: Batter rheological behaviour as well as the ability of sugar substitutes to increase starch gelatinisation temperature proved to be controlling factors of the textural properties and volume of the cakes. The sensory evaluation indicated that overall acceptance followed closely the scores of tenderness and taste. Copyright © 2011 Society of Chemical Industry
Dark chocolate acceptability: influence of cocoa origin and processing conditions
Authors: Torres‐Moreno Miriam , Tarrega Amparo , Costell Elvira , Blanch Consol
Published: August 2011

BACKGROUND: Chocolate properties can vary depending on cocoa origin, composition and manufacturing procedure, which affect consumer acceptability. The aim of this work was to study the effect of two cocoa origins (Ghana and Ecuador) and two processing conditions (roasting time and conching time) on dark chocolate acceptability.

RESULTS: Overall acceptability and acceptability for different attributes (colour, flavour, odour and texture) were evaluated by 95 consumers. Differences in acceptability among dark chocolates were mainly related to differences in flavour acceptability. The use of a long roasting time lowered chocolate acceptability in Ghanaian samples while it had no effect on acceptability of Ecuadorian chocolates. This response was observed for most consumers (two subgroups with different frequency consumption of dark chocolate). However, for a third group of consumers identified as distinguishers, the most acceptable dark chocolate samples were those produced with specific combinations of roasting time and conching time for each of the cocoa geographical origin considered.

CONCLUSION: To produce dark chocolates from a single origin it is important to know the target market preferences and to select the appropriate roasting and conching conditions. Copyright © 2011 Society of Chemical Industry
Non‐varnishing and tribological characteristics of polyalkylene glycol‐based synthetic turbine fluid
Authors: Khemchandani Govind
Published: August 2011

Varnish build‐up in heavy duty gas turbines is a leading cause of costly unplanned shutdowns and resulting lost power generation capacity. The culprit is the conventional petroleum‐based turbine oil, which breaks down to form varnish and sludge that cause servo valves to stick. Use of filtration to remove solid degradation by‐products addresses a symptom but not the root cause of varnish formation: the petroleum‐based turbine oils themselves. For the best protection against varnish‐related shutdowns, a switch from petroleum‐based turbine oil to non‐varnishing polyalkylene glycol (PAG)‐based synthetic turbine fluid was undertaken by four power plants in North America. PAG‐based synthetic turbine fluid chemistry, its tribological characteristics and successful trials in GE 7FA heavy duty gas turbines (General Electric Company, Fairfield, CT, USA) are discussed in this paper. PAG‐based synthetic turbine fluid has outperformed the hydrocarbon turbine oil in reduced sludge and varnish formation due to its polar nature and solvating power in plant trials as well as in a modified ASTM D 2893 test. Copyright © 2011 John Wiley & Sons, Ltd.
Photo‐assisted peptide enrichment in protein complex cross‐linking analysis of a model homodimeric protein using mass spectrometry
Authors: Yan Funing , Che Fa‐Yun , Nieves Edward , Weiss Louis M. , Angeletti Ruth H. , Fiser Andras
Published: August 2011

MS analysis of cross‐linked peptides can be used to probe protein contact sites in macromolecular complexes. We have developed a photo‐cleavable cross‐linker that enhances peptide enrichment, improving the signal‐to‐noise ratio of the cross‐linked peptides in mass spectrometry analysis. This cross‐linker utilizes nitro‐benzyl alcohol group that can be cleaved by UV irradiation and is stable during the multiple washing steps used for peptide enrichment. The enrichment method utilizes a cross‐linker that aids in eliminating contamination resulting from protein‐based retrieval systems, and thus, facilitates the identification of cross‐linked peptides. Homodimeric pilM protein from Pseudomonas aeruginosa 2192 (pilM) was investigated to test the specificity and experimental conditions. As predicted, the known pair of lysine side chains within 14 Å was cross‐linked. An unexpected cross‐link involving the protein's amino terminus was also detected. This is consistent with the predicted mobility of the amino terminus that may bring the amino groups within 19 Å of one another in solution. These technical improvements allow this method to be used for investigating protein–protein interactions in complex biological samples.
Proteomic analysis of extracellular matrices used in stem cell culture
Authors: Hughes Chris S. , Radan Lida , Betts Dean , Postovit Lynne M. , Lajoie Gilles A.
Published: August 2011

Numerous matrices for the growth of human embryonic stem cells (hESC) in vitro have been described. However, their exact composition is typically unknown. Information on the components of these matrices will aid in the development of a fully defined growth surface for hESCs. These matrices typically consist of mixture of proteins present in a wide range of abundance making their characterization challenging. In this study, we performed the proteomic analysis of five previously uncharacterized matrices: CellStart, Human Basement Membrane Extract (Human BME), StemXVivo, Bridge Human Extracellular Matrix (BridgeECM), and mouse embryonic fibroblast conditioned matrix (MEF‐CMTX). Based on a proteomics protocol optimized using lysates from HeLa cells, we undertook the analysis of the five complex extracellular matrix (ECM) samples using a combination of strong anion and cation exchange chromatography and SDS‐PAGE. For each of these matrices, we identify numerous proteins, indicating their complex nature. We also compared these results with a similar proteomics analysis of the growth matrix, Matrigel™. From these analyses, we observed that fibronectin is a primary component of nearly all hESC supportive matrices. This observation led to the investigation of the suitability of fibronectin as a defined ECM for the growth of hESCs. We found that fibronectin promotes the maintenance of pluripotent H9 and CA1 hESCs in an undifferentiated state using mTeSR1 medium. This finding validates the utility of characterizing matrices used for hESC growth in revealing ECM components required for culturing hESCs in a universally applicable defined system.
Can the false‐discovery rate be misleading?
Authors: Barboza Rodrigo , Cociorva Daniel , Xu Tao , Barbosa Valmir C. , Perales Jonas , Valente Richard H. , França Felipe M. G. , Yates John R. , Carvalho Paulo C.
Published: August 2011

The decoy‐database approach is currently the gold standard for assessing the confidence of identifications in shotgun proteomic experiments. Here, we demonstrate that what might appear to be a good result under the decoy‐database approach for a given false‐discovery rate could be, in fact, the product of overfitting. This problem has been overlooked until now and could lead to obtaining boosted identification numbers whose reliability does not correspond to the expected false‐discovery rate. To overcome this, we are introducing a modified version of the method, termed a semi‐labeled decoy approach, which enables the statistical determination of an overfitted result.
Photosynthetic reaction center protein in nanostructures
Authors: Hajdu Kata , Szabó Tibor , Magyar Melinda , Bencsik Gábor , Németh Zoltán , Nagy Krisztina , Magrez Arnaud , Forró László , Váró György , Hernádi Klára , Nagy László
Published: August 2011

Photosynthetic reaction center (RC) is one of the most important proteins, because it is Nature's solar battery converting light energy into chemical potential in the photosynthetic membrane assuring conditions for carbon reduction in cells. Although it is developed in nanometer scale, and is working in nanoscopic power, this is the protein that assures the energy input practically for the whole biosphere on Earth. The extremely large quantum yield of the primary charge separation (close to 100%) in the RC offers a big challenge to use it in nanodevices. Results of structural (AFM, EM), optical, and electro chemical investigations on RC bio‐nanocomposite materials based on different carrier matrices (e.g., CNTs, ITO) will be presented.
Growth of catalyst‐assisted and catalyst‐free horizontally aligned single wall carbon nanotubes
Authors: Ibrahim Imad , Bachmatiuk Alicja , Rümmeli Mark H. , Wolff Ulrike , Popov Alexey , Boltalina Olga , Büchner Bernd , Cuniberti Gianaurelio
Published: August 2011

Here, we report the growth of homogenously horizontally aligned single wall carbon nanotubes on stable temperature cut single crystal quartz using chemical vapor deposition with controllable yield and length from binary metallic mixtures as well as fullerene derivatives. We manage the yield and length of the as‐grown tubes on stable temperature cut single crystal quartz by controlling the surface roughness of the support substrates by thermal treatment in air. Carbon caps derived from pre‐treated fullerenes are also explored for their potential to nucleate growth of single wall carbon nanotubes without the need of a catalyst particle. Exohedrally functionalized fullerenes are apparently better nucleators than C60 fullerenes.

Yield of the as‐grown single wall carbon nanotubes on thermally annealed ST‐quartz substrates.

magnified image
Reproductive outcomes in women with congenital uterine anomalies: a systematic review
Authors: Chan Y. Y. , Jayaprakasan K. , Tan A. , Thornton J. G. , Coomarasamy A. , Raine‐Fenning N. J.
Published: August 2011

Objective

Congenital uterine anomalies are common but their effect on reproductive outcome is unclear. We conducted a systematic review to evaluate the association between different types of congenital uterine anomaly and various reproductive outcomes.

Methods

Searches were performed using MEDLINE, EMBASE, the Cochrane Library and Web of Science. The Newcastle‐Ottawa Quality Assessment Scale was used for quality assessment. Uterine defects were grouped into arcuate uteri, canalization defects (septate and subseptate uteri) and unification defects (unicornuate, bicornuate and didelphys uteri). Pooled risk ratios (RR) with 95% confidence intervals (CI) were computed using random effects models.

Results

We identified nine studies comprising 3805 women. Meta‐analysis showed that arcuate uteri were associated with increased rates of second‐trimester miscarriage (RR, 2.39; 95% CI, 1.33–4.27, P = 0.003) and fetal malpresentation at delivery (RR, 2.53; 95% CI, 1.54–4.18; P < 0.001). Canalization defects were associated with reduced clinical pregnancy rates (RR, 0.86; 95% CI, 0.77–0.96; P = 0.009) and increased rates of first‐trimester miscarriage (RR, 2.89; 95% CI; 2.02–4.14; P < 0.001), preterm birth (RR, 2.14; 95% CI, 1.48–3.11; P < 0.001) and fetal malpresentation (RR, 6.24; 95% CI, 4.05–9.62; P < 0.001). Unification defects were associated with increased rates of preterm birth (RR, 2.97; 95% CI, 2.08–4.23; P < 0.001) and fetal malpresentation (RR, 3.87; 95% CI, 2.42–6.18; P < 0.001).

Conclusions

Canalization defects reduce fertility and increase rates of miscarriage and preterm delivery. None of the unification defects reduces fertility but some are associated with miscarriage and preterm delivery. Arcuate uteri are specifically associated with second‐trimester miscarriage. All uterine anomalies increase the chance of fetal malpresentation at delivery. Copyright © 2011 ISUOG. Published by John Wiley & Sons, Ltd.
Emerging applications of nanotechnology for the diagnosis and management of vulnerable atherosclerotic plaques
Authors: Yu Shann S. , Ortega Ryan A. , Reagan Brendan W. , McPherson John A. , Sung Hak‐Joon , Giorgio Todd D.
Published: August 2011

An estimated 16 million people in the United States have coronary artery disease (CAD), and approximately 325,000 people die annually from cardiac arrest. About two‐thirds of unexpected cardiac deaths occur without prior recognition of cardiac disease. A vast majority of these deaths are attributable to the rupture of ‘vulnerable atherosclerotic plaques’. Clinically, plaque vulnerability is typically assessed through imaging techniques, and ruptured plaques leading to acute myocardial infarction are treated through angioplasty or stenting. Despite significant advances, it is clear that current imaging methods are insufficiently capable for elucidating plaque composition—which is a key determinant of vulnerability. Further, the exciting improvement in the treatment of CAD afforded by stenting procedures has been buffered by significant undesirable host‐implant effects, including restenosis and late thrombosis. Nanotechnology has led to some potential solutions to these problems by yielding constructs that interface with plaque cellular components at an unprecedented size scale. By leveraging the innate ability of macrophages to phagocytose nanoparticles, contrast agents can now be targeted to plaque inflammatory activity. Improvements in nano‐patterning procedures have now led to increased ability to regenerate tissue isotropy directly on stents, enabling gradual regeneration of normal, physiologic vascular structures. Advancements in immunoassay technologies promise lower costs for biomarker measurements, and in the near future, may enable the addition of routine blood testing to the clinician's toolbox—decreasing the costs of atherosclerosis‐related medical care. These are merely three examples among many stories of how nanotechnology continues to promise advances in the diagnosis and treatment of vulnerable atherosclerotic plaques. WIREs Nanomed Nanobiotechnol 2011 3 620–646 DOI: 10.1002/wnan.158

This article is categorized under:

Diagnostic Tools > In Vitro Nanoparticle-Based Sensing

Implantable Materials and Surgical Technologies > Nanomaterials and Implants

Therapeutic Approaches and Drug Discovery > Nanomedicine for Cardiovascular Disease
Do enzyme activities during decomposition follow predicted patterns? A test of the conceptual model of litter decay.
Authors: Rinkes Zachary , Weintraub Michael , DeForest Jared , Moorhead Daryl
Published: August 2011

Surprisingly, there remains a paucity of research examining specific interactions between the relationship between microbial community behavior and plant litter chemistry during decomposition. A more mechanistic understanding of the relationship between these drivers will ultimately help determine the trajectory of litter decomposition and the conditions in which soils serve as either a source or sink for atmospheric C. In order to examine these relationships, a laboratory incubation was established using Acer saccharum litter and a sandy soil (< 1.5% organic matter). Extracellular enzyme activities ([BETA]-glucosidase, N-acetyl glucosaminidase, leucine-amino peptidase, acid phosphatase, phenol oxidase, and peroxidase) were monitored on a consistent basis along with instantaneous rates of carbon dioxide production, microbial biomass (carbon and nitrogen) and phospholipid fatty acid biomarkers (PLFA), and nitrogen and phosphorus availability. Microbial biomass and microbial respiration peaked within the first week of the experiment. This was likely due to the high availability of water soluble substrates early in decay that can be obtained without the production of extracellular enzymes. [BETA]-glucosidase (BG), N-acetyl glucosaminadase (NAG), and acid phosphatase activities increased quickly following the first week and peaked within the first month (at approximately 15% mass loss). Leucine amino peptidase was not detected during the incubation, which may be due to its strong positive correlation with soil pH, while other hydrolytic enzymes tend to track concentrations of soil organic matter. Phenol oxidase and peroxidase activities were not measurable until the second month of the experiment (> 25% mass loss), likely following the depletion of more labile substrates. A second increase in BG activity was observed between Days 83-111, which may be due to an increase in the availability of cellulose that was previously shielded by lignin, since oxidative enzyme activity was first detected on Day 68. We also observed some shifts in microbial PLFAs along with enzyme activities during decomposition. Prior to the increases in enzyme activity we observed a high proportion of PLFA 18:1[omega]7c, which is a bacterial biomarker. As enzyme activities increased, we observed a decrease in this biomarker and an increase in 18:2[omega]6,9c, a fungal biomarker that was correlated with BG and NAG activity. We did not observe any clear relationships between PLFAs and lignolytic enzyme activity, however. Overall, we observed a distinct functional shift in microbial substrate use that may be associated with either changes in composition of the microbial community or community shifts in enzyme production.
Nuclear Fuel Cycles: Interfaces with the Environment
Authors: Sharrad Clint A. , Harwood Laurence M. , Livens Francis R.
Published: August 2011

The waste materials generated in the nuclear fuel cycle are very varied, ranging from the tailings arising from mining and processing uranium ore, depleted uranium in a range of chemical forms, to a range of process wastes of differing activities and properties. Indeed, the wastes generated are intimately linked to the options selected in operating the nuclear fuel cycle, most obviously to the management of spent fuel. An open fuel cycle implies the disposal of highly radioactive spent fuel, whereas a closed fuel cycle generates a complex array of waste streams. On the other hand, a closed fuel cycle offers options for waste management, for example reduction in highly active waste volume, decreased radiotoxicity, and removal of fissile material. Many technological options have been proposed or explored, and each brings its own particular mix of wastes and environmental challenges.
Management of Land Contaminated by the Nuclear Legacy
Authors: Kimber Richard , Livens Francis R. , Lloyd Jonathan R.
Published: August 2011

The widespread spread use of nuclear materials over the past 60 years has lead to anthropogenic release of radionuclides into the environment. The release of such contaminants is currently of great public concern and scientific interest worldwide. Contamination has arisen on sites involved in both military and civilian uses of nuclear material through leakages, spills, controlled discharges and munitions use. The management of this nuclear legacy is a global priority as governments seek to decommission and reclaim land contaminated by the use of nuclear facilities. The scale of contamination presents a serious financial burden with the cleanup of US sites expected to cost up to a trillion dollars. In the UK, the problem exists on a smaller but significant scale with associated cleanup costs estimated to be in the order of £100 billion. A wide range of disciplines are required to understand the behaviour of radionuclides and co-contaminants in these contaminated environments in order for effective remediation techniques to be utilised. Potential remediation strategies cover a range of biological, chemical and physical methods which can be used to treat the complex contamination scenarios found at nuclear sites. A number of these remediation techniques have been trialled at several sites managed by the United States Department of Energy with some success in treating radionuclide contamination.
Micro-Raman spectroscopy of laser processed YBa2Cu3O7-δ thin films
Authors: Barboy I. , Camerlingo C. , Bar I. , Bareli G. , Jung G.
Published: August 2011

The oxygen content and the local oxygen arrangement of laser processed YBa2Cu3O7-δ (YBCO) thin films grown on LaAlO3 substrates have been probed by micro-Raman spectroscopy On these films, channels for easy vortex motion have been laser written (LW) into the bridge constrictions by heat-induced, partial depletion of oxygen from the laser-illuminated areas of these films. Raman microscopy has been used to investigate and characterize the oxygen content and structure of the laser written channels. Direct evidence for local micro-structural changes in the film during the LW process is presented and the heat affected zone, surrounding the channel borders, has been mapped.
Coevolution of inverse cascade and nonlinear heat front in shear flows of strongly coupled Yukawa liquids
Authors: J. Ashwin , Ganesh R.
Published: August 2011

Using classical molecular dynamics (MD) simulations, we report on the development and propagation of a nonlinear heat front in parallel shear flows of a strongly coupled Yukawa liquid. At a given coupling strength, a subsonic shear profile is superposed on an equilibrated Yukawa liquid and Kelvin Helmholtz (KH) instability is observed. Coherent vortices are seen to emerge towards the nonlinear regime of the instability. It is seen that while inverse cascade leads to a continuous transfer of flow energy towards the largest scales, there is also a simultaneous transfer of flow energy into the thermal velocities of grains at the smallest scale. The latter is an effect of velocity shear and thus leads to the generation of a nonlinear heat front. In the linear regime, the heat front is seen to propagate at speed much lesser than the adiabatic sound speed of the liquid. Spatio-temporal growth of this heat front occurs concurrently with the inverse cascade of KH modes.
Simulation of dust streaming in toroidal traps: Stationary flows
Authors: Reichstein Torben , Piel Alexander
Published: August 2011

Molecular-dynamic simulations were performed to study dust motion in a toroidal trap under the influence of the ion drag force driven by a Hall motion of the ions in E × B direction, gravity, inter-particle forces, and friction with the neutral gas. This article is focused on the inhomogeneous stationary streaming motion. Depending on the strength of friction, the spontaneous formation of a stationary shock or a spatial bifurcation into a fast flow and a slow vortex flow is observed. In the quiescent streaming region, the particle flow features a shell structure which undergoes a structural phase transition along the flow direction.
Lie algebraic approach and quantum treatment of an anisotropic charged particle via the quadratic invariant
Authors: Abdalla M. Sebawe , Leach P. G. L.
Published: August 2011

We consider the problem of a charged harmonic oscillator under the influence of a constant magnetic field. The system is assumed to be anisotropic and the magnetic field is applied along z-axis. A canonical transformation is invoked to remove the interaction term and the system is reduced to a model contains two uncoupled harmonic oscillators. Two classes of real and complex quadratic invariants (constants of motion) are obtained. We employ the Lie algebraic technique to find the most general solution for the wave-function for both real and complex invariants. The quadratic invariant is also used to derive two classes of creation and annihilation operators from which the wave-functions in the coherent states and number states are obtained. Some discussion related to the advantage of using the quadratic invariants to solve the Cauchy problem instead of the direct use of the Hamiltonian itself is also given.
Probing energy transfer in an ensemble of silicon nanocrystals
Authors: Jayatilleka H. , Diamare D. , Wojdak M. , Kenyon A. J. , Mokry C. R. , Simpson P. J. , Knights A. P. , Crowe I. , Halsall M. P.
Published: August 2011

Time-resolved photoluminescence measurements of silicon nanocrystals formed by ion implantation of silicon into silicon dioxide reveal multi-exponential luminescence decays. Three discrete time components are apparent in the rise and decay data, which we associate with different classes of nanocrystals. The values of decay time are remarkably constant with emission energy, but the relative contributions of the three components vary strongly across the luminescence band. In keeping with the quantum confinement model for luminescence, we assign emission at high energies to small nanocrystals and that at low energies to large nanocrystals. By deconvolving the decay data over the full emission band, it is possible to study the migration of excitation from smaller (luminescence donor) to larger (luminescence acceptor) nanocrystals. We propose a model of diffusion of excitation between neighboring nanocrystals, with long lifetime emission being from the largest nanocrystal in the local neighborhood. Our data also allow us to study the saturation of acceptor nanocrystals, effectively switching off excitation transfer, and Auger recombination in non-interacting nanocrystals.