bluuebunny/crossref_metadata_2025 huggingface dataset:
Fatty acids and bioactive compounds of the pulps and kernels of Brazilian palm species, guariroba (Syagrus oleraces), jerivá (Syagrus romanzoffiana) and macaúba (Acrocomia aculeata)
Authors: Coimbra Michelle C , Jorge Neuza
Published: September 2011

BACKGROUND: Bioactive compounds are capable of providing health benefits, reducing disease incidence or favoring body functioning. There is a growing search for vegetable oils containing such compounds. This study aimed to characterize the pulp and kernel oils of the Brazilian palm species guariroba (Syagrus oleracea), jerivá (Syagrus romanzoffiana) and macaúba (Acrocomia aculeata), aiming at possible uses in several industries.

RESULTS: Fatty acid composition, phenolic and carotenoid contents, tocopherol composition were evaluated. The majority of the fatty acids in pulps were oleic and linoleic; macaúba pulp contained 526 g kg−1 of oleic acid. Lauric acid was detected in the kernels of all three species as the major saturated fatty acid, in amounts ranging from 325.8 to 424.3 g kg−1. The jerivá pulp contained carotenoids and tocopherols on average of 1219 µg g−1 and 323.50 mg kg−1, respectively.

CONCLUSION: The pulps contained more unsaturated fatty acids than the kernels, mainly oleic and linoleic. Moreover, the pulps showed higher carotenoid and tocopherol contents. The kernels showed a predominance of saturated fatty acids, especially lauric acid. The fatty acid profiles of the kernels suggest that these oils may be better suited for the cosmetic and pharmaceutical industries than for use in foods. Copyright © 2011 Society of Chemical Industry
Broad bean and pea by‐products as sources of fibre‐rich ingredients: potential antioxidant activity measured in vitro
Authors: Mateos‐Aparicio Inmaculada , Redondo‐Cuenca Araceli , Villanueva‐Suárez María‐José
Published: September 2011

BACKGROUND By‐products generated during the processing of plant food can be considered a promising source of dietary fibre as a functional compound. The dietary fibre composition, soluble sugars and antioxidant activity of the extractable polyphenols of pea and broad bean by‐products have been analysed in this study.

RESULTS: Total dietary fibre using AOAC methods plus hydrolysis (broad bean pod: 337.3 g kg−1; pea pod: 472.6 g kg−1) is higher (P < 0.05) in both by‐products than with the Englyst method (broad bean pod: 309.7 g kg−1; pea pod: 434.6 g kg−1). The main monomers are uronic acids, glucose, arabinose and galactose in broad bean pods. However, pea pods are very rich in glucose and xylose. The soluble sugars analysed by high‐performance liquid chromatography in both by‐products have glucose as the most important component, followed by sucrose and fructose. The ferric reducing antioxidant power (broad bean pod: 406.4 µmol Trolox equivalents g−1; pea pod: 25.9 µmol Trolox equivalents g−1) and scavenging effect on 2,2‐diphenyl‐1‐picrylhydrazyl radical (EC50 of broad bean pod: 0.4 mg mL−1; EC50 of pea pod: 16.0 mg mL−1) were also measured.

CONCLUSIONS: Broad bean and pea by‐products are very rich in dietary fibre, particularly insoluble dietary fibre and their extractable polyphenols demonstrate antioxidant activity. Therefore they might be regarded as functional ingredients. Copyright © 2011 Society of Chemical Industry
Functional role of human laryngeal nerve connections
Authors: Martin‐Oviedo Carlos , Maranillo Eva , Lowy‐Benoliel Alejandro , Pascual‐Font Aran , Martinez‐Guirado Tomas , Rodriguez‐Niedenführ Marc , Sañudo Jose , Scola Bartolome , Vazquez Teresa
Published: September 2011

Objectives/Hypothesis:

Current knowledge of the functional role of human laryngeal nerves is based on traditional laryngeal neuroanatomic descriptions or contradictory electromyographic studies. The aim of this study was to clarify the functional role of neural connections between laryngeal nerves by correlating the different electromyographic patterns observed after laryngeal stimulation and the existence of different neural connections.

Study Design:

Descriptive.

Methods:

Electromyographic and morphologic study in 13 patients during total laryngectomy procedure.

Results:

Seven patients showed an additional evoked response from the cricothyroid muscle after recurrent laryngeal nerve stimulation. External laryngeal nerve stimulation resulted in additional responses from the posterior cricoarytenoid muscle in three cases and from the arytenoid muscle in one. The presence of a neural connection was confirmed in all patients who showed an unexpected electromyographic response.

Conclusions:

The different connections between laryngeal nerves are at least partially of motor nature and play a role in the mobility of vocal folds.
Fighting against diffraction: apodization and near field diffraction structures
Authors: Wang H. , Sheppard C.J.R. , Ravi K. , Ho S.T. , Vienne G.
Published: September 2011

Diffraction is a natural phenomenon, which occurs when waves propagate or encounter an obstacle. Diffraction is also a fundamental aspect of modern optics: all imaging systems are diffraction systems. However, like a coin has two sides, diffraction also leads to some unfavorable effects, such as an increase in the size of a beam during propagation, and a limited minimal beam size after focusing. To overcome these disadvantages set by diffraction, many techniques have been developed by various groups, including apodization techniques to reduce the divergence of a laser beam and increase the resolution, and time reversal, STED microscopy, super lenses and optical antennas to obtain resolution down to nano‐scale. This review concentrates on the diffraction of electromagnetic waves, and the ways to overcome beam divergence and the diffraction limit.
Dendritic Carrier Based on PEG: Design and Degradation of Acid‐sensitive Dendrimer‐like Poly(ethylene oxide)s
Authors: Feng Xiaoshuang , Chaikof Elliot L. , Absalon Christelle , Drummond Carlos , Taton Daniel , Gnanou Yves
Published: September 2011

Degradable dendrimer‐like PEOs were designed using an original ABC‐type branching agent featuring a cleavable ketal group, following an iterative divergent approach based on the anionic ring opening polymerization (AROP) of ethylene oxide and arborization of PEO chain ends. A seventh generation dendrimer‐like PEO carrying 192 peripheral hydroxyls and exhibiting a molar mass of 446 kg · mol−1 was obtained in this way. The chemical degradation of these dendritic scaffolds was next successfully accomplished under acidic conditions, forming linear PEO chains of low molar mass (≈2 kg · mol−1), as monitored by 1H NMR, SEC, and MALDI‐TOF mass spectrometry as well as by AFM.

magnified image
Morphometrical Analysis on Cut Marks Using a 3D Digital Microscope
Authors: Boschin F. , Crezzini J.
Published: September 2011

Microscopic analysis represents a powerful tool for understanding taphonomy. Our work, as in other studies, aims to identify the origin of different kinds of marks on bones. In this paper, we test the application of a HIROX Digital Microscope KH‐7700. This microscope captures 3D images of the bone surface, thus bringing into focus the whole section of striations. This enables the direct observation of their shape from several points of view and the relatively rapid procurement of a variety of measurements (e.g. depth, breadth, angles). This technology has been applied to several butchery experiments, in which both stone and metal tools have been used to produce cut marks on skeletal elements. The morphometrical parameters presented in this paper enabled the correct identification of the different origins of experimental striations and were further tested on two archaeological sets of cut marks inflicted by both metal blades and flint flakes or tools. Therefore, the obtained experimental records constitute a useful database for archaeological remains. The morphometrical parameters developed and implemented in this study represent objective criteria for identifying the origin of cut marks which can be processed through statistical analysis. Copyright © 2011 John Wiley & Sons, Ltd.
The Diagnosis and Context of a Facial Deformity from an Anglo‐Saxon Cemetery at Spofforth, North Yorkshire
Authors: Craig E. , Craig G.
Published: September 2011

An individual aged between 6 and 7 years at death from a 7th to 9th century cemetery at Village Farm, Spofforth, North Yorkshire, presented significant pathological swelling to the left facial bones. The ectocranial surface was bulbous and uneven, and the expanded diploë was densely packed with a mass of thick trabeculae. Radiographic and histological analysis, in combination with the macroscopically observed pathological changes, supported the differential diagnosis of fibrous dysplasia. The skeletal changes to the left face and jaw would have resulted in a significant facial deformity. Examples of individuals with physical impairments or disfigurements from Anglo‐Saxon cemeteries are rare. Nevertheless, it seems that a significant proportion are afforded unusual burial practices more often associated with deviancy, for example, at the edge of cemeteries or on a reversed orientation, seemingly indicating that their diminished physical capabilities or altered physical appearance had a detrimental effect on their social status. The child from Spofforth was, however, buried in a normative manner, extended, supine and in a plain earth‐cut grave, with no indication that their facial deformity had prompted unusual funerary provision. This example of facial disfigurement contributes to a growing corpus of potentially disabled individuals from early medieval England. Copyright © 2011 John Wiley & Sons, Ltd.
Voluntary environmental programs: A comparative perspective
Authors: Prakash Aseem , Potoski Matthew
Published: September 2011

Voluntary environmental programs (VEPs) are institutions for inducing firms to produce environmental goods beyond legal requirements. A comparative perspective on VEPs shows how incentives to sponsor and participate in VEPs vary across countries in ways that reveal their potential and limitations. Our brief survey examines conditions under which VEPs emerge, attract participants, and improve participants' environmental performance. We focus on the costs and bene‐fits for actors seeking to supply (or sponsor) these governance mechanisms as well as the costs and benefits for firms who are considering joining VEPs and adhering to their program obligations. © 2011 by the Association for Public Policy Analysis and Management.
Synthesis of gradient polymer by using polysiloxane‐based photoinitiator
Authors: Lai Xiu‐hua , Sun Fang , Yin Rui‐Xue , Ma Gui‐Ping , Nie Jun
Published: September 2011

This paper reported a polysiloxane‐based photoinitiator (184‐AC‐Si), which was synthesized basing on traditional photoinitiator 1‐hydroxy‐cyclohexyl phenyl ketene (184) and polysiloxane. Its structure was confirmed by Hydrogen‐1 nuclear magnetic resonance (1H NMR), real‐time infrared spectroscopy and gel permeation chromatography (GPC). Ultraviolet (UV) absorption spectra of 184‐AC‐Si showed a red‐shifted maximum absorption compared with 184. The kinetics of photopolymerization was studied by real‐time infrared spectroscopy. More importantly, because of the polysiloxane‐based photoinitiator had good ability to float up, which could be proved by X‐ray photoelectron spectroscopy, mapping energy dispersive spectroscopy, UV absorption, and GPC measurements, a convenient and simple method for preparing gradient polymer initiated by 184‐AC‐Si was successfully developed. Copyright © 2011 John Wiley & Sons, Ltd.
Sorafenib and cisplatin/doxorubicin (PLADO) in pediatric hepatocellular carcinoma
Authors: Schmid Irene , Häberle Beate , Albert Michael H. , Corbacioglu Selim , Fröhlich Birgit , Graf Norbert , Kammer Birgit , Kontny Udo , Leuschner Ivo , Scheel‐Walter Hans‐Gerhard , Scheurlen Wolfram , Werner Sebastian , Wiesel Thomas , von Schweinitz Dietrich
Published: September 2011

Purpose

Overall survival is poor in children with primary unresectable hepatocellular carcinoma. Sorafenib has been shown to significantly improve progression‐free survival in adult hepatocellular carcinoma (HCC) patients. We evaluated the experience of PLADO (cisplatin 80 mg/m2/day, doxorubicin 2 × 30 mg/m2/day) in combination with sorafenib in pediatric HCC patients.

Patients and Methods

Clinical data of 12 patients (7–16 years), 7 with unresectable tumor, were retrospectively assessed.

Results

In total 6/12 (50%) patients are in complete remission after a median follow‐up of 20 months (4 with PLADO/sorafenib/resection, 2 with liver transplantation after local relapse). Of the seven patients with unresectable tumor, PLADO/sorafenib resulted in partial response (PR) in four, stable disease (SD) in two, and progression in one. Three are alive in CR after complete resection after 12 (alternative therapy after two cycles PLADO/sorafenib), 12 and 18 months (six cycles PLADO/sorafenib), respectively. All four patients with elevated alpha‐fetoprotein levels had a marked drop after two cycles. Of the five patients with primary complete tumor resection one is alive disease‐free at 27 months. Four had local or metastatic relapses (13, 7, 12, and 13 months), two of whom were rescued by liver transplantation (CR after 25 and 32 months). The main toxicity attributable to sorafenib was a hand–foot skin reaction (HFSR) in seven patients.

Conclusion

Sorafenib in combination with PLADO may be a promising approach in pediatric HCC; HFSR was the most important toxicity. Data based on prospective studies are needed to evaluate pharmacokinetics, resectability rates, and survival in pediatric HCC treated with sorafenib. Pediatr Blood Cancer 2012; 58: 539–544. © 2011 Wiley Periodicals, Inc.
Durable complete response to chemotherapy in an infant with a clival chordoma
Authors: Al‐Rahawan Mohamad M. , Siebert James D. , Mitchell Craig S. , Smith Stephen D.
Published: September 2011

Chordomas are rare bone tumors of notochord remnants that may occur anywhere within the axial skeleton. The standard of care is complete surgical removal. Proton beam irradiation is commonly used when the tumor is inaccessible or has recurred. Chemotherapy has been used in the treatment of patients at relapse but it has been generally proven ineffective. We report a 7‐month‐old infant with a clival chordoma who responded to combination chemotherapy consisting of cycles of vincristine/cyclophosphamide/doxorubicin alternating with etoposide/ifosfamide. She has been off chemotherapy for 2 years and is well at age 5. Pediatr Blood Cancer 2012;59:323–325. © 2011 Wiley Periodicals, Inc.
Incidence, clinical features, and risk factors of idiopathic pneumonia syndrome following hematopoietic stem cell transplantation in children
Authors: Sakaguchi Hirotoshi , Takahashi Yoshiyuki , Watanabe Nobuhiro , Doisaki Sayoko , Muramatsu Hideki , Hama Asahito , Shimada Akira , Yagasaki Hiroshi , Kudo Kazuko , Kojima Seiji
Published: September 2011

Background

Idiopathic pneumonia syndrome (IPS) is a severe complication that can occur after hematopoietic stem cell transplantation (HSCT) and is often associated with a fatal outcome despite intensive supportive care.

Procedure

To assess the incidence and risk factors of IPS, we reviewed 251 consecutive patients (median age, 7.0 years) who received HSCT at the Department of Pediatrics, Nagoya University Hospital, between January 1990 and July 2009.

Results

Twenty of 251 (cumulative incidence of IPS at 2 years after HSCT, 8.0%; 95% confidence interval (CI), 5.1–12.4%) patients developed IPS. The median duration from HSCT to diagnosis of IPS was 67 days (range, 12–486 days). Patients with IPS had significantly higher 5‐year transplant‐related mortality compared to patients without IPS (52% (95% CI, 19–77%) vs. 13% (95% CI, 5–25%), P < 0.001), and the probability of 5‐year overall survival was significantly worse for patients with IPS (42% (95% CI, 25–64%) vs. 68% (95% CI, 59–76%), P = 0.01). By multivariate analysis, high risk in underlying disease (HR, 2.5; 95% CI, 1.0–6.7; P = 0.05) and a busulfan‐containing regimen (HR, 3.5; 95% CI, 1.3–9.9; P < 0.01) were identified as the independent risk factors for developing IPS.

Conclusion

The prophylactic strategies for IPS in patients with these risk factors were warranted. Pediatr Blood Cancer 2012; 58: 780–784. © 2011 Wiley Periodicals, Inc.
Neuroblastoma progress on many fronts: The neuroblastoma research symposium
Authors: Wylie Luke , Philpott Anna
Published: September 2011

Neuroblastoma (NBL) is a pediatric tumor of infancy derived from precursor cells of the sympathetic nervous system. Clinicians and researchers in developmental biology and genetics recently met to facilitate meaningful crosstalk and to discuss considerable progress made in the clinical treatment and basic biology of NBL. For instance, discoveries in familial NBL have identified genetic aberrations in Phox2b and Alk that predispose to NBL, while advances in epigenetics and MYCN regulation have also offered insight into NBL pathogenesis and future treatment. Moreover, novel therapeutic avenues are also being explored, including targeted immunotherapies, and innovative radiotherapeutic and chemotherapeutic approaches. This multi‐disciplinary meeting was convened to aid the transfer of new biological findings into the clinic and to use clinical advances to inform the basic biological understanding of this devastating disease. Pediatr Blood Cancer 2012; 58: 649–651. © 2011 Wiley Periodicals, Inc.
Frequency and determinants of potential drug‐drug interactions in an elderly population receiving regular home visits by GPs ‐ results of the home medication review in the AGnES‐studies
Authors: Hoffmann Wolfgang , van den Berg Neeltje , Thyrian Jochen René , Fiss Thomas
Published: September 2011

Purpose

There is limited knowledge about prevalence and determinants of potential drug‐drug‐interactions (pDDI) in the ambulatory health care setting. In this manuscript we analysed the prevalence and determinants of pDDI in the AGnES home visit population (GP‐supporting, community‐based, e‐health‐assisted, systemic intervention).

Methods

779 Home‐dwelling patients received an IT‐supported home medication review (HMR). The interaction monographs of the ABDA‐database were used to identify pDDI. A binary multivariate logistic regression model was used to analyse determinants for occurrence of moderate and serious pDDI, respectively.

Results

Patients (mean age f: 79.8 yrs; m: 76.2 yrs) took a mean number of 6.8 active substances (SD = 3.3) regularly. 626 patients (80.4%) with an HMR had at least one pDDI (mean = 4.8; SD = 4.4). In 454 patients (58.3%) we found at least one pDDI with moderate or serious relevance (mean = 2.9; SD = 2.8). The most frequent moderate pDDI was the combination of potassium excretion diuretics (e.g. hydrochlorothiazide) with anti‐inflammatory drugs (e.g. ibuprofen; n = 258 patients). Adjusted for age and gender, multiple binary logistic regression showed significant results for the number of taken active substances (continuous variable; OR = 1.48; 95%‐CI 1.382‐1.585), metabolic diseases (OR = 1.52; 95%‐CI 1.039‐2.223), a diagnose of a muscular‐skeletal disease (OR = 1.741; 95%‐CI 1.204‐2.517), infectious disease (OR = 0.127; 95%‐CI 0.021‐0.783), and gastro‐intestinal disease (OR = 0.538; 95%‐CI 0.322‐0.899).

Conclusion

Using a comprehensive, computer‐assisted HMR in an ambulatory care setting we have identified a high proportion of pDDI of moderate or serious clinical relevance. These pDDI require an intervention from intensified monitoring to a change in medication. Further investigations should focus on clinical outcome of pDDI. Copyright © 2011 John Wiley & Sons, Ltd.
The Temporal Reciprocity of Values and Beliefs: A Longitudinal Study within a Major Life Transition
Authors: Goodwin Robin , Polek Ela , Bardi Anat
Published: September 2011

Values and beliefs (or social axioms) are important personality constructs, but little previous work has examined the relationship between the two, and none has examined their real–life longitudinal effects on one another. Major life transitions—such as moving to a new culture—can challenge existing values and beliefs and therefore provide a particularly useful context for the analysis of value and belief change. The main aim of this research was to examine whether values may predict theoretically meaningful belief change and vice versa. Polish migrants participated in the study shortly after their arrival in the UK and at two, subsequent, nine–month intervals ( N = 172). Cross–lagged effects suggested reciprocal effects of values and beliefs, depending on the value involved. Findings are discussed in light of current debates over personality change, as well as the broader impact of significant life transitions on personality. Copyright © 2011 John Wiley & Sons, Ltd.
Well‐defined diblock copolymers possessing fluorescent and metal chelating functionalities as novel macromolecular sensors for amines and metal ions
Authors: Demetriou Maria , Krasia‐Christoforou Theodora
Published: September 2011

The amino‐ and metal‐ion sensing capability of a novel type of well‐defined block copolymers based on 9‐anthrylmethyl methacrylate (AnMMA; hydrophobic, fluorescent) and 2‐(acetoacetoxy)ethyl methacrylate (AEMA; hydrophobic, metal chelating) has been investigated in organic media. AEMAx‐b‐AnMMAy diblock copolymers were prepared for the first time using reversible addition‐fragmentation chain transfer (RAFT) polymerization. All polymers were characterized in terms of molecular weights, polydispersity indices and compositions by size exclusion chromatography and 1H NMR spectroscopy, respectively. The glass transition (Tg) temperatures of the AEMAx and AnMMAx homopolymers and the AEMAx‐b‐AnMMAy diblock copolymers were determined using differential scanning calorimetry. These systems were evaluated toward their ability to act as effective dual chemosensors (i.e., amino‐ and metal‐ion sensors) in an organic solvent (chloroform). More precisely, the fluorescence intensity of both the AnMMAx homopolymers and the AnMMAx‐b‐AEMAy diblock copolymers in solution exhibited a significant decrease in the presence of triethylamine. Moreover, the presence of iron (III) cations were also found to significantly affect the fluorescence signal of the anthracene moieties when those were combined in a block copolymer structure with the AEMA units, due to complex formation occurring between the β‐ketoester groups of the AEMAx segment and the cations. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012
Micromechanical models of young's modulus of NR/organoclay nanocomposites
Authors: Lowe David J. , Chapman Andrew V. , Cook Stuart , Busfield James J. C.
Published: September 2011

Small strain Young's moduli of natural rubber (NR)/organoclay nanocomposites were estimated using the Guth–Gold, Halpin–Tsai (HT), and Krieger–Dougherty (KD) models, and compared with experimental measurements of NR vulcanizates containing organo‐montmorillonite (OM) or organo‐sepiolite (OS). To account for the effect on modulus of the NR matrix of the vulcanization‐active modifier in the organoclay, a matrix modulus correction (MMC) term was derived from the vulcanization parameters of the nanocomposites. The KD model gave a better empirical fit with the experimental data than the Guth–Gold model, with both giving good agreement with particle shape factors estimated from transmission electron microscope (TEM) images. The HT model gave the best fit with experiment for both types of nanocomposite, and use of the MMC term meant that the empirical shape factor was sufficiently close to that estimated from TEM images that the model could potentially be used to accurately predict the Young's moduli of NR/OM and NR/OS nanocomposites. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 49: 1621–1627, 2011
Ghrelin receptor as a novel imaging target for prostatic neoplasms
Authors: Lu Chen , McFarland Mark S. , Nesbitt Rae‐Lynn , Williams Andrew K. , Chan Susanne , Gomez‐Lemus Jose , Autran‐Gomez Anna Maria , Al‐Zahrani Ali , Chin Joseph L. , Izawa Jonathan I. , Luyt Leonard G. , Lewis John D.
Published: September 2011

BACKGROUND

Ghrelin is a natural growth hormone secretagogue (GHS) that is co‐expressed with its receptor GHSR in human prostate cancer (PCa) cells. Imaging probes that target receptors for ghrelin may delineate PCas from benign disease. The specificity of a novel ghrelin‐imaging probe for PCa over normal tissue or benign disease was assessed.

METHODS

A fluorescein‐bearing ghrelin analogue was synthesized (fluorescein‐ghrelin(1–18)), and its application for imaging was evaluated in a panel of PCa cell lines and human prostate tissue. Prostate core biopsy samples were collected from fresh surgery specimens of 13 patients undergoing radical prostatectomy. Ghrelin probe signal was detected and quantified in each sample using a hapten amplification technique and associated with pathological features.

RESULTS

The ghrelin probe was taken up by GHSR‐expressing LNCaP and PC‐3 cells, and not in BPH cells that express low levels of GHSR. Binding was blocked by competition with excess unlabeled probe. The ghrelin probe signal was 4.7 times higher in PCa compared to benign hyperplasia tissue (P = 0.0027) and normal tissue (P = 0.0093). Furthermore, while the ghrelin probe signal was 1.9‐fold higher in PIN compared to benign hyperplasia (P = 0.0022) and normal tissue (P = 0.0047), there was no significant difference in the signal of benign hyperplasia compared to normal tissue.

CONCLUSION

The imaging probe fluorescein‐ghrelin(1–18) is specific for PCa, and did not associate significantly with benign hyperplasia or normal prostate tissue. This data suggests that ghrelin analogues may be useful as molecular imaging probes for prostatic neoplasms in both localized and metastatic disease. Prostate 72:825–833, 2012. © 2011 Wiley Periodicals, Inc.
On the use of distance constraints in protein–protein docking computations
Authors: Shih Edward S. C. , Hwang Ming‐Jing
Published: September 2011

Protein–protein docking (PPD) is a computational process that predicts the structure of a complex of two interacting proteins from their unbound structures. The accuracy of PPD predictions is low, but can be greatly enhanced if experimentally determined distance data are available for incorporation into the prediction. However, the specific effects of distance constraints on PPD predictions are largely uncharacterized. In this study, we systematically simulated the effects of using distance constraints both on a new distance constraint‐driven PPD approach, called DPPD, and also, by re‐ranking, on a well‐established grid‐based global search approach. Our results for a PPD benchmark dataset of 84 protein complexes of known structures showed that near 100% docking success rates could be obtained when the number of distance constraints exceeded six, the degrees of freedom of the system, but the success rate was significantly reduced by long distance constraints, large binding‐induced conformational changes, and large errors in the distance data. Our results also showed that, under most conditions simulated, even two or three distance constraints were sufficient to achieve a much better success rate than those using a sophisticated physicochemical function to re‐rank the results of the global search. Our study provides guidelines for the practical incorporation of experimental distance data to aid PPD predictions. Proteins 2012;. © 2011 Wiley Periodicals, Inc.
Template‐based protein structure modeling using TASSERVMT
Authors: Zhou Hongyi , Skolnick Jeffrey
Published: September 2011

Template‐based protein structure modeling is commonly used for protein structure prediction. Based on the observation that multiple template‐based methods often perform better than single template‐based methods, we further explore the use of a variable number of multiple templates for a given target in the latest variant of TASSER, TASSERVMT. We first develop an algorithm that improves the target‐template alignment for a given template. The improved alignment, called the SP3alternative alignment, is generated by a parametric alignment method coupled with short TASSER refinement on models selected using knowledge‐based scores. The refined top model is then structurally aligned to the template to produce the SP3alternative alignment. Templates identified using SP3threading are combined with the SP3alternative and HHEARCH alignments to provide target alignments to each template. These template models are then grouped into sets containing a variable number of template/alignment combinations. For each set, we run short TASSER simulations to build full‐length models. Then, the models from all sets of templates are pooled, and the top 20–50 models selected using FTCOM ranking method. These models are then subjected to a single longer TASSER refinement run for final prediction. We benchmarked our method by comparison with our previously developed approach, pro‐sp3‐TASSER, on a set with 874 easy and 318 hard targets. The average GDT‐TS score improvements for the first model are 3.5 and 4.3% for easy and hard targets, respectively. When tested on the 112 CASP9 targets, our method improves the average GDT‐TS scores as compared to pro‐sp3‐TASSER by 8.2 and 9.3% for the 80 easy and 32 hard targets, respectively. It also shows slightly better results than the top ranked CASP9 Zhang‐Server, QUARK and HHpredA methods. The program is available for download athttp://cssb.biology.gatech.edu/. © 2011 Wiley Periodicals, Inc.
Progress in the prediction of pKavalues in proteins
Authors: Alexov Emil , Mehler Ernest L. , Baker Nathan , M. Baptista António , Huang Yong , Milletti Francesca , Erik Nielsen Jens , Farrell Damien , Carstensen Tommy , Olsson Mats H. M. , Shen Jana K. , Warwicker Jim , Williams Sarah , Word J. Michael
Published: September 2011

The pKa‐cooperative aims to provide a forum for experimental and theoretical researchers interested in protein pKavalues and protein electrostatics in general. The first round of the pKa‐cooperative, which challenged computational labs to carry out blind predictions against pKas experimentally determined in the laboratory of Bertrand Garcia‐Moreno, was completed and results discussed at the Telluride meeting (July 6–10, 2009). This article serves as an introduction to the reports submitted by the blind prediction participants that will be published in a special issue ofPROTEINS: Structure, Function and Bioinformatics. Here, we briefly outline existing approaches for pKacalculations, emphasizing methods that were used by the participants in calculating the blind pKavalues in the first round of the cooperative. We then point out some of the difficulties encountered by the participating groups in making their blind predictions, and finally try to provide some insights for future developments aimed at improving the accuracy of pKacalculations. Proteins 2011; © 2011 Wiley‐Liss, Inc.
CASP9 target classification
Authors: Kinch Lisa N. , Shi Shuoyong , Cheng Hua , Cong Qian , Pei Jimin , Mariani Valerio , Schwede Torsten , Grishin Nick V.
Published: September 2011

The Critical assessment of protein structure prediction round 9 (CASP9) aimed to evaluate predictions for 129 experimentally determined protein structures. To assess tertiary structure predictions, these target structures were divided into domain‐based evaluation units that were then classified into two assessment categories: template based modeling (TBM) and template free modeling (FM). CASP9 targets were split into domains of structurally compact evolutionary modules. For the targets with more than one defined domain, the decision to split structures into domains for evaluation was based on server performance. Target domains were categorized based on their evolutionary relatedness to existing templates as well as their difficulty levels indicated by server performance. Those target domains with sequence‐related templates and high server prediction performance were classified as TMB, whereas those targets without identifiable templates and low server performance were classified as FM. However, using these generalizations for classification resulted in a blurred boundary between CASP9 assessment categories. Thus, the FM category included those domains without sequence detectable templates (25 target domains) as well as some domains with difficult to detect templates whose predictions were as poor as those without templates (five target domains). Several interesting examples are discussed, including targets with sequence related templates that exhibit unusual structural differences, targets with homologous or analogous structure templates that are not detectable by sequence, and targets with new folds. Proteins 2011; © 2011 Wiley‐Liss, Inc.
The pKa Cooperative: A collaborative effort to advance structure‐based calculations of pKa values and electrostatic effects in proteins
Authors: Nielsen Jens E. , Gunner M. R. , García‐Moreno E. Bertrand
Published: September 2011

The pKa Cooperative (http://www.pkacoop.org) was organized to advance development of accurate and useful computational methods for structure‐based calculation of pKa values and electrostatic energies in proteins. The Cooperative brings together laboratories with expertise and interest in theoretical, computational, and experimental studies of protein electrostatics. To improve structure‐based energy calculations, it is necessary to better understand the physical character and molecular determinants of electrostatic effects. Thus, the Cooperative intends to foment experimental research into fundamental aspects of proteins that depend on electrostatic interactions. It will maintain a depository for experimental data useful for critical assessment of methods for structure‐based electrostatics calculations. To help guide the development of computational methods, the Cooperative will organize blind prediction exercises. As a first step, computational laboratories were invited to reproduce an unpublished set of experimental pKa values of acidic and basic residues introduced in the interior of staphylococcal nuclease by site‐directed mutagenesis. The pKa values of these groups are unique and challenging to simulate owing to the large magnitude of their shifts relative to normal pKa values in water. Many computational methods were tested in this first Blind Prediction Challenge and critical assessment exercise. A workshop was organized in the Telluride Science Research Center to objectively assess the performance of many computational methods tested on this one extensive data set. This volume of Proteins: Structure, Function, and Bioinformatics introduces the pKa Cooperative, presents reports submitted by participants in the Blind Prediction Challenge, and highlights some of the problems in structure‐based calculations identified during this exercise. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Electrical transport in strained MgxZn1−xO:P thin films grown by pulsed laser deposition on ZnO(000‐1)
Authors: Brandt Matthias , Bonholzer Michael , Stölzel Marko , Benndorf Gabriele , Spemann Daniel , Lorenz Michael , Grundmann Marius
Published: September 2011

Phosphorus‐doped MgxZn1−xO thin films with various Mg content (0.07 ≤ x ≤ 0.28) and up to 0.7 at% P were grown on ZnO(000‐1) single crystals by pulsed laser deposition (PLD). In dependence on the dopant concentrations, tensile or compressively strained, in‐plane lattice matched, i.e., pseudomorphic growth of the MgZnO:P films was confirmed by high‐resolution X‐ray diffraction (HR‐XRD). All investigated, high‐quality MgZnO:P films are n‐type, also after post‐growth annealing at 850 °C. From the Hall analysis the activation energy of the dominating donors was derived, yielding values of up to 345 meV for high oxygen partial pressure during growth, and shallow donors with an activation energy of about 30 meV for low oxygen pressure. The Hall‐mobility of the MgxZn1−xO:P films at a temperature of 65 K was as high as 740 cm2/Vs, and reached values up to 190 cm2/Vs at room temperature, close to the best values reported for bulk ZnO.
Flow‐dependent background‐error covariances for a convective‐scale data assimilation system
Authors: Brousseau Pierre , Berre Loïk , Bouttier François , Desroziers Gérald
Published: September 2011

AROME‐France is a convective‐scale numerical weather prediction system which has been running operationally at Météo‐France since the end of 2008. It uses a 3D‐Var assimilation scheme in order to determine its initial conditions. Static background‐error covariances are calculated for the 3D‐Var using differences between AROME forecasts from an ensemble data assimilation. In this study, the covariance calculation is generalized in order to estimate time‐dependent background‐error covariances. A six‐member ensemble is shown to provide robust covariance estimates in the context of the considered homogeneous covariance formulation. There is significant day‐to‐day variability in the variances, autocorrelations, and cross‐correlations of background errors. This variability is linked to the meteorological conditions over the AROME‐France model domain. The benefits of using flow‐dependent background‐error covariances, instead of static ones, are shown using assimilation diagnostics and measures of forecast performance. Copyright © 2011 Royal Meteorological Society
Ensemble prediction and parameter estimation system: the concept
Authors: Järvinen Heikki , Laine Marko , Solonen Antti , Haario Heikki
Published: September 2011

This paper discusses algorithmic estimation of numerical weather prediction (NWP) model closure parameters which appear in physical parametrizations of sub‐grid scale processes. Currently, these parameters are specified manually. Our hypothesis is that the NWP model forecast skill is sensitive to the specified parameter values. Therefore some parameter value combinations score better than others, but it is very demanding to manually specify the optimal combination. First, we approximate the number of test forecasts that would be needed to estimate the posterior probability densities of a limited number of closure parameters, in a spirit of the Bayesian parameter estimation approach. Second, we discuss various options to accommodate the related huge computational task; we end up proposing that operational ensemble prediction might be a potential host. Third, we analyse the ensemble prediction system characteristics from the parameter estimation point of view. We rule out various standard parameter estimation methods; instead we suggest an estimation concept that can be on‐line coupled with existing ensemble prediction systems to utilize the operational ensemble simulations. Thus practically no additional computations are introduced. Such a method, the ensemble prediction and parameter estimation system (EPPES), is developed here and demonstrated in low‐order numerical tests in the companion paper (Laine M, Solonen A, Haario H, Järvinen H. 2011. Q. J. R. Meteorol. Soc. DOI: 10.1002/qj.922). Copyright © 2011 Royal Meteorological Society
Quantitative analysis of remedial approaches, costs, and time required to remediate dry cleaner sites
Authors: Luis Steven J. , King Stacey L. , Zandipour Nazgol , Koenigsberg Stephen S.
Published: September 2011

This article presents an analysis of remedial approaches, costs, and time required to remediate dry cleaner sites in the United States based on data compiled by the State Coalition for the Remediation of Dry Cleaners (SCRD). Trends in soil and groundwater remedy selection are identified and discussed. Median costs and the time required to remediate dry cleaner sites are presented. In addition, median costs and the duration of soil and groundwater remediation for the most widely used remedial approaches are reported. The analysis is intended to serve the needs of stakeholders, including responsible parties, consultants, regulators, and litigants, as well as real estate developers, banks, and other holders of portfolios of impacted dry cleaner sites by providing quantitative results useful for planning and transactional analysis. © 2011 Wiley Periodicals, Inc.
Field‐scale uranium (VI) bioimmobilization monitored by lipid biomarkers and 13C‐acetate incorporation
Authors: Peacock Aaron D. , Hedrick David B. , Long Philip E. , Nevin Kelly P. , Resch Charles T. , Lovley Derek R. , White David C.
Published: September 2011

At the Old Rifle uranium mill‐tailing site in eastern Colorado, a test of subsurface amendment with acetate to stimulate the reductive immobilization of uranium was monitored by using lipid biomarker analysis and incorporation of 13C‐labeled acetate into lipid biomarkers. Both sediment and groundwater samples were analyzed. Within 7 days of acetate addition, groundwater microbial biomass increased by a factor of 5, and remained higher than control values in most samples for the 28 days sampled. At 29 days after the beginning of acetate amendment, 4 of 12 sediment samples had microbial biomass greater than the 95 percent confidence interval of controls. The mole percents of the phospholipid fatty acids 16:1ω7c and 16:1ω5c increased over control values upon acetate amendment, and incorporated high levels of 13C from labeled acetate in groundwater and sediment samples. 16:1ω7c is a biomarker for Geobacter, and evidence is provided that 16:1ω5c represents an unidentified iron‐reducing bacterium, probably a member of the Desulfobulbaceae. Biomarkers for organisms other than iron‐reducing bacteria, iso‐ and anteiso‐branched fatty acids and 18:1ω9c, decreased upon acetate amendment, and had their highest stable isotope incorporation at least 4 days after labeled acetate amendment ended, evidence for carbon‐sharing between iron‐reducers and other microorganisms. © 2011 Wiley Periodicals, Inc.
Monte Carlo simulation of secondary electron images for real sample structures in scanning electron microscopy
Authors: Zhang P. , Wang H. Y. , Li Y. G. , Mao S. F. , Ding Z. J.
Published: September 2011

Monte Carlo simulation methods for the study of electron beam interaction with solids have been mostly concerned with specimens of simple geometry. In this article, we propose a simulation algorithm for treating arbitrary complex structures in a real sample. The method is based on a finite element triangular mesh modeling of sample geometry and a space subdivision for accelerating simulation. Simulation of secondary electron image in scanning electron microscopy has been performed for gold particles on a carbon substrate. Comparison of the simulation result with an experiment image confirms that this method is effective to model complex morphology of a real sample. SCANNING 34: 145–150, 2012. © 2011 Wiley Periodicals, Inc.
Cellular Uptake and Cytotoxic Impact of Chemically Functionalized and Polymer‐Coated Carbon Nanotubes
Authors: Ali‐Boucetta Hanene , Al‐Jamal Khuloud T. , Müller Karin H. , Li Shouping , Porter Alexandra E. , Eddaoudi Ayad , Prato Maurizio , Bianco Alberto , Kostarelos Kostas
Published: September 2011

The impact of nanomaterials such as carbon nanotubes on biological matter is a topic of increasing interest and concern and requires a multifaceted approach to be resolved. A modified cytotoxic (lactate dehydrogenase (LDH)) assay is developed in an attempt to offer a valid and reliable methodology for screening carbon nanotube toxicity in vitro. Two of the most widely used types of surface‐modified multiwalled carbon nanotubes (MWNTs) are tested: ammonium‐functionalized MWNTs (MWNT‐NH3+) and Pluronic F127 coated MWNTs (MWNT:F127). Chemically functionalized MWNTs show significantly greater cellular uptake into lung epithelial A549 cells compared to the non‐covalently Pluronic F127‐coated MWNTs. In spite of this, MWNT:F127 exhibit enhanced cytotoxicity according to the modified LDH assay. The validity of the modified LDH assay is further validated by direct comparison with other less reliable or accurate cytotoxicity assays. These findings indicate the reliability of the modified LDH assay as a screening tool to assess carbon nanotube cytotoxicity and illustrate that high levels of carbon nanotube cellular internalization do not necessarily lead to adverse responses.
Effect of Nitrogen and Niobium on the Structure and Secondary Hardening of Super Hard High Speed Tool Steel
Authors: Halfa Hossam , Eissa Mamdouh , El‐Fawakhry Kamal , Mattar Taha
Published: September 2011

High‐speed steels have been used mostly for multi‐point cutting tools and for plastic working tools. High speed steels are ferrous based alloys of the Fe‐C‐X multi‐component system where X represents a group of alloying elements comprising mainly Cr, W or Mo, V, and Co. The properties of these steels can be improved by modifying their chemical composition or the technology of their production. One of the new trends in modifying the tool steels chemical composition consists in the addition of niobium and nitrogen. In this work, the effects of niobium and nitrogen on morphology of carbides and secondary hardening temperature of investigated high speed tool steels were studied. This experimental work shows that, the conventional ingots have many types of carbides of different shapes and sizes precipitate on the boundary together with thick needle like carbides. On the contrary, for nitrogen steel, the nitrogen alloying leads to form dense, fine and well distributed microstructure. While, on the case of niobium alloying, single carbide (MC), and different types of eutectic carbides were precipitated which have a major effect on the secondary hardening temperature.
Correlation of tape location and tension with surgical outcome after transobturator suburethral tape procedures
Authors: Yang J.‐M. , Yang S.‐H. , Huang W.‐C. , Tzeng C.‐R.
Published: September 2011

Objective

To explore, using 4D ultrasound, the importance of location and tension of transobturator sub‐ urethral tape (TOT) with respect to surgical outcome.

Methods

Enrolled into the study were 56 women who had undergone TOT placement in the treatment of urodynamic stress incontinence. Tape location and tension were assessed by 4D ultrasound with the women at rest, during straining and during coughing. Ultrasound parameters representing tape location included the sagittal tape–symphysis pubis distance (sTSD), sagittal tape–symphysis pubis angle (sTSA) and tape percentile (an indication of tape position along the urethra with respect to urethral length), while those representing tape tension included urethral encroachment, sagittal tape–urethra distances at the upper end (sTUDu), center (sTUDc) and lower end (sTUDl) of the tape and axial urethral central echolucent area at the tape center (aUCEAc).

Results

In women in whom the tape procedure had been successful, during increased intra‐abdominal pressure sTSA and the incidence of urethral encroachment increased, while sTUDu, sTUDc, sTUDl and aUCEAc decreased. Compared with those reporting no stress urinary incontinence (SUI) symptoms, women who reported SUI postoperatively had lower tape percentile. Women with SUI postoperatively demonstrated no manifestation on ultrasound of urethral encroachment at rest or during increased intra‐abdominal pressure. Women with postoperative overactive bladder (OAB) symptoms had shorter resting sTSD and larger resting sTSA than did women without OAB symptoms. Women reporting postoperative de novo or worsening voiding difficulty had larger resting sTSA and higher incidence of urethral encroachment at rest than did women without this difficulty.

Conclusions

Both tape location and tape tension are associated with surgical outcome of TOT procedures. Assessment of tape location and tension can be achieved using 4D ultrasound. Copyright © 2012 ISUOG. Published by John Wiley & Sons, Ltd.