bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oligo(N‐alkoxy glycines): Trans substantiating peptoid conformations
Authors: Jordan Peter A. , Paul Bishwajit , Butterfoss Glenn L. , Renfrew P. Douglas , Bonneau Richard , Kirshenbaum Kent 
Published: May 2011

AbstractPeptoid oligomers possess many desirable attributes as bioactive peptidomimetic agents, including their ease of synthesis, chemical diversity, and capability for molecular recognition. Ongoing efforts to develop functional peptoids will necessitate improved capability for control of peptoid structure, particularly of the backbone amide conformation. We introduce alkoxyamines as a new reagent for solid phase peptoid synthesis. Herein, we describe the synthesis of N‐alkoxy peptoids, and present NMR data indicating that the oligomers adopt a single stable conformation featuring trans amide bonds. These findings, combined with results from computational modeling, suggest that N‐alkoxy peptoid oligomers have a strong propensity to adopt a polyproline II type secondary structure. © 2011 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 96: 617–626, 2011.
Search for identical octapeptides in unrelated proteins: Structural plasticity revisited
Authors: M. Saravanan K. , Selvaraj S. 
Published: May 2011

AbstractSince proteins are dynamic in nature, they can alter their local structure in response to changes in their environment factors such as temperature, pH, phosphorylation, and binding of other small molecules. These conformational changes are extremely important for the correct folding and functioning of proteins. There are also a number of diseases associated with protein conformational change such as amyloid diseases. To stimulate research into the above factors which specify one conformation over another, different theoretical models have been proposed and tested against sequence similar distant structure protein fragments. In order to simplify the computational complexity of identifying conformational changes in proteins, various local sequence search algorithms were employed and the structural plasticity in unrelated proteins was examined by various research groups. In the present work, we revisit the mechanism of structural plasticity in unrelated proteins with increased number of structures in Protein Data Bank by comparing identical octapeptides in unrelated proteins with dictionary of protein secondary structure extracted from existing experimental data. Our goal is to bring out the influence of hydrophobic residues, hydrophilic residues, flanking residues, difference in secondary structural propensities of surrounding residues, difference in phi‐psi angles and local and nonlocal interactions in identical octapeptides adopting different conformations. Also we have used surrounding hydrophobicity, environment dependent interaction energy, atomic mean force potential, structural unit contacts and difference profiles models to explore the factors which cause structural plasticity. The results discussed here may provide insights into protein folding, design and function. © 2011 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 98: 11–26, 2012.
Cholecystectomy as a risk factor for oesophageal adenocarcinoma
Authors: Lagergren J , Mattsson F 
Published: May 2011

Abstract

Background
Owing to an increased risk of oesophageal bile exposure after cholecystectomy, an association with oesophageal adenocarcinoma is possible. There are some data in support of this hypothesis, and the aim of this study was to ascertain whether the association could be confirmed.

Methods
A population-based cohort study was undertaken to compare the number of cases of oesophageal adenocarcinoma observed in a cohort of patients who have had a cholecystectomy in Sweden during 1965–2008 with the expected number, calculated from the entire Swedish population of corresponding age, sex and year. The risk of oesophageal adenocarcinoma was assessed by calculating the standardized incidence ratio (SIR) with 95 per cent confidence intervals.

Results
The cholecystectomy cohort included 345 251 patients who were followed up for a mean of 15 years and contributed 4 854 969 person-years at risk. The total of 126 new cases of oesophageal adenocarcinoma was greater than expected (SIR 1·29, 1·07 to 1·53). The strength of the association between cholecystectomy and oesophageal adenocarcinoma tended to increase with longer follow-up after cholecystectomy. There was no association between cholecystectomy and oesophageal squamous cell carcinoma (SIR 0·93, 0·81 to 1·08), and in an unoperated cohort of 192 960 patients with gallstones no increased risk of oesophageal adenocarcinoma was identified (SIR 0·99, 0·71 to 1·35).

Conclusion
Cholecystectomy appears to be linked to an increased risk of oesophageal adenocarcinoma, but the absolute risk is small.
Dietary red palm oil protects the heart against the cytotoxic effects of anthracycline
Authors: Wergeland A. , Bester D. J. , Sishi B. J. N. , Engelbrecht A. M. , Jonassen A. K. , Van Rooyen J. 
Published: May 2011

Strong anti‐neoplastic anthracyclines like daunorubicin (DNR) and doxorubicin (DOX) have high efficacy against systemic neoplasm and solid tumours. However, clinically, they cause chronic cardiomyopathy and congestive heart failure. Red palm oil (RPO) supplementation can protect the heart against ischemic injury. We therefore hypothesize that supplementation with RPO during chemotherapy may protect the heart.Control rats received a standard diet, and the experimental group received RPO in addition for 4 weeks. Each group was subsequently injected with either saline or DNR over a 12‐day period towards the end of 4 weeks. Hearts were excised and perfused on a working heart system. Functional parameters were measured. Tissue samples were collected for analysis of mRNA and protein levels. DNR + RPO increased aortic output by 25% (p < 0·05) compared with DNR only. Furthermore, DNR treatment significantly reduced tissue mRNA levels of superoxide dismutase 1 (SOD1) and nitric oxide synthase 1 (NOS1) compared with untreated controls. Protein expression of SOD1 followed the same pattern as mRNA levels. NOS1 protein levels were significantly increased in DNR treated rats when compared with untreated controls. In addition, DNR increased phosphorylation of p38 and Jun N‐terminal kinase compared with untreated controls, whereas DNR + RPO completely counteracted this activation. DNR + RPO significantly up regulated the protein extracellular signal‐regulated kinase 1 level compared with DNR only.In this model of DNR treatment, RPO is associated with stabilization of important antioxidant enzymes such NOS and SOD, and inhibition of the ‘stress’ induced mitogen‐activated protein kinase pathways. Dietary RPO also maintained function, similar to control, in DNR treated hearts. Copyright © 2011 John Wiley & Sons, Ltd.
Quantum‐Sized Gold Nanoclusters: Bridging the Gap between Organometallics and Nanocrystals
Authors: Jin Rongchao , Zhu Yan , Qian Huifeng 
Published: May 2011

AbstractThis Concept article provides an elementary discussion of a special class of large‐sized gold compounds, so‐called Au nanoclusters, which lies in between traditional organogold compounds (e.g., few‐atom complexes, <1 nm) and face‐centered cubic (fcc) crystalline Au nanoparticles (typically >2 nm). The discussion is focused on the relationship between them, including the evolution from the Au⋅⋅⋅Au aurophilic interaction in AuI complexes to the direct AuAu bond in clusters, and the structural transformation from the fcc structure in nanocrystals to non‐fcc structures in nanoclusters. Thiolate‐protected Aun(SR)m nanoclusters are used as a paradigm system. Research on such nanoclusters has achieved considerable advances in recent years and is expected to flourish in the near future, which will bring about exciting progress in both fundamental scientific research and technological applications of nanoclusters of gold and other metals.
The Stepwise Diels–Alder Reaction of 4‐Nitrobenzodifuroxan with Danishefsky’s Diene
Authors: Steglenko Dmitry V. , Kletsky Mikhail E. , Kurbatov Sergey V. , Tatarov Artem V. , Minkin Vladimir I. , Goumont Regis , Terrier François 
Published: May 2011

AbstractThe Diels–Alder reaction of 4‐nitrobenzodifuroxan (NBDF) with 1‐methoxy‐3‐trimethylsilyloxy‐1,3‐butadiene has been investigated experimentally and theoretically. Treatment of NBDF with excess diene in chloroform at room temperature was found to afford a single product that contained a carbonyl functionality. Based on an X‐ray structure and NMR spectroscopic data, the product appeared to be a result of the hydrolysis of the OSiMe3 moiety of the thermodynamically more stable endo [2+4] cycloadduct, characterized by a cis arrangement of the MeO and NO2 functionalities. In situ NMR investigations of the interaction were carried out at room temperature in CDCl3 and at −40 °C in deuterated acetonitrile. Calculations at the B3LYP/6‐31G* level in the gas phase and in acetonitrile were carried out under the assumption that the most stable cis conformation of the diene is also the most reactive in the interaction. The analysis revealed the NBDF/cis diene interaction involves the formation of a zwitterionic intermediate. Importantly, this intermediate is formed in two preferred conformations, which correspond to the endo and exo modes of approach of the reagents. Cyclization of these two identified conformations afforded the experimentally characterized endo and exo [2+4] cycloadducts. According to the calculations, the interconversion of the two conformers can either take place through a return to the pre‐reaction complexes or it can occur by rotation through an intermediate conformation of lesser stability. In view of the stepwise character of the interaction, the possibility that the intermediate zwitterion is the result of the interaction between NBDF and the trans diene could not be excluded. Calculations carried out with the most stable and more populated s‐trans conformer confirmed this idea and supported the role of the zwitterion in the overall interaction.
A Highly Selective, Cell‐Permeable Fluorescent Nanoprobe for Ratiometric Detection and Imaging of Peroxynitrite in Living Cells
Authors: Tian Jiangwei , Chen Huachao , Zhuo Linhai , Xie Yanxia , Li Na , Tang Bo 
Published: May 2011

AbstractPeroxynitrite (ONOO−) is a highly reactive species implicated in the pathology of numerous diseases and there is currently great interest in developing fluorescent probes that can selectively detect ONOO− in living cells. Herein, a polymeric micelle‐based and cell‐penetrating peptide‐coated fluorescent nanoprobe that incorporates ONOO− indicator dye and reference dye for the ratiometric detection and imaging of ONOO− has been developed. The nanoprobe effectively avoids the influences from enzymatic reaction and high‐concentration .OH and ClO−. The improved ONOO− selectivity of the nanoprobe is achieved by a delicate complementarity of properties between the nanomatrix and the embedded molecular probe (BzSe‐Cy). This nanoprobe also has other attractive properties, such as good water solubility, photostability, biocompatibility, and near‐infrared excitation and emission. Fluorescence imaging experiments by confocal microscopy show that this nanoprobe is capable of visualizing ONOO− produced in living cells and it exhibits very low toxicity and good membrane permeability. We anticipate that this technique will be a potential tool for the precise pathological understanding and diagnosis of ONOO−‐related human diseases.
The Role of the N‐Terminal Domain in the Regulation of the “Constitutively Active” Conformation of Protein Kinase CK2α: Insight from a Molecular Dynamics Investigation
Authors: Cristiani Andrea , Costa Giorgio , Cozza Giorgio , Meggio Flavio , Scapozza Leonardo , Moro Stefano 
Published: May 2011

AbstractProtein kinase CK2 is an extremely well‐conserved pleiotropic protein kinase with a growing list of substrates, the majority of which are proteins implicated in signal transduction, gene expression, and transcription‐related functions. Protein kinase CK2 is a ubiquitous heterotetrameric serine/threonine protein kinase made up of two α or α’ catalytic subunits and two β regulatory subunits. Moreover, protein kinase CK2 is defined as a “constitutively active” protein kinase in contrast to most other protein kinases characterized by the presence of distinct conformations associated with the active and inactive states. As previously demonstrated by in vitro mutation studies, CK2 activity is substantially regulated by the interaction between the N‐terminal tail and the kinase domain. In fact, progressive deletions of the N‐terminal tail show a decrease in the activity of the kinase. Even if the detrimental effects of Δ2–12 deletion can be partially reversed by the addition of a CK2β subunit, deletions Δ2–12 and Δ2–30 progressively decrease the basal activity of CK2. In particular, as experimentally demonstrated, the Δ2–12 N‐terminal deletion affects both the KM value for ATP and for the substrate peptide, and the kcat value of CK2α. In this work, molecular dynamics (MD) simulations were carried out on wild‐type (wt), Δ2–12 and Δ2–30 deletion mutants of CK2α in order to explore the role of the N‐terminal tail on the conformational behavior of CK2. Furthermore, classical MD simulations were carried out to assess the anticipated impact of conformational changes in a novel set of CK2α mutant forms, such as the triple mutant Y206F‐R10A‐Y261F and the single mutant Y125F.
The Capacity to See Things from the Child's Point of View—Assessing Insightfulness in Mothers with and without a Diagnosis of Depression
Authors: Quitmann Julia H. , Kriston Levente , Romer Georg , Ramsauer Brigitte 
Published: May 2011

Insightfulness is seen as the mental capacity that provides the context for a secure child–parent attachment. It involves the ability to see things from the child's perspective and is based on insight into the child's motives, a complex view of the child and openness to new information about the child. To test our hypothesis that maternal insightfulness is related to maternal depression, we utilized the Insightfulness Assessment (IA) developed by Oppenheim and Koren‐Karie to conduct and analyse interviews in which mothers discussed their perceptions of video segments of their interactions with their children. We compared the results of a control group of 30 mothers without a diagnosis of depression with a sample of 23 mothers diagnosed with depression (International Classification of Diseases, 10th Revision). As expected, depression was negatively related to maternal insightfulness.Oppenheim and Koren‐Karie have argued that the IA might be used as a diagnostic instrument; our work suggests that the IA might show ways of aiding mothers in improving the quality of mother–infant interaction while they are being treated for depression. Copyright © 2011 John Wiley & Sons, Ltd.Key Practitioner Message

Insightfulness is seen as the mental capacity that provides the context for a secure child–parent attachment.
Maternal depression was negatively related to maternal insightfulness.
The Insightfulness Assessment might be used as a diagnostic instrument.
The Insightfulness Assessment might show ways of aiding mothers in improving the quality of mother‐infant interaction while they are being treated for depression.
Bisquinoxaline‐Fused Porphyrins for Dye‐Sensitized Solar Cells
Authors: Imahori Hiroshi , Iijima Hiroaki , Hayashi Hironobu , Toude Yuuki , Umeyama Tomokazu , Matano Yoshihiro , Ito Seigo 
Published: May 2011

Abstract5,10,15,20‐Tetrakis(2,4,6‐trimethylphenyl)‐6′‐carboxylquinoxalino[2,3‐b]quinoxalino[12,13‐b′]porphyrinatozinc(II) (ZnPBQ) is synthesized to evaluate the effects of π elongation of quinoxaline‐fused porphyrins on the optical, electrochemical, and photovoltaic properties. ZnPBQ showed an intensified Soret band as well as red‐shifted Soret and Q bands relative to 5,10,15,20‐tetrakis(2,4,6‐trimethylphenyl)‐6′‐carboxylquinoxalino[2,3‐b]porphyrinatozinc(II) (ZnPQ), demonstrating the improved light‐harvesting property of ZnPBQ. The optical and electrochemical HOMO–LUMO gaps were consistent with those estimated by DFT calculations. The photovoltaic properties were compared under optimized conditions, in which a sealed device structure with TiCl4‐treated, TiO2 double layers was used. The ZnPBQ cell exhibited a relatively high power conversion efficiency (η) of 4.7 %, which was smaller than that of the ZnPQ cell (η=6.3 %). The weaker electronic coupling between the LUMO of ZnPBQ and conduction band (CB) of TiO2 or more tilted geometry of ZnPBQ on the TiO2 surface may result in the low electron injection/charge collection efficiency as well as the low incident photon‐to‐current efficiency (IPCE) for the ZnPBQ cell (maximum IPCE=56 %) relative to the ZnPQ cell (maximum IPCE=75 %), leading to the lower η value of the ZnPBQ cell than that of the ZnPQ cell. In addition, the open‐circuit potential of the ZnPBQ cell also slightly decreased with the effect of charge recombination from the electrons injected into the CB of TiO2 to I3−.
Toxoplasmosis in a post‐transplant bronchoalveolar lavage: A case report
Authors: Monaco Sara E. , Monaghan Sara A. , Stamm Jason A. , Khalbuss Walid E. , Nichols Larry , Pantanowitz Liron 
Published: May 2011

AbstractToxoplasma gondii usually causes an asymptomatic and then latent infection in human adults; however, a potentially fatal disseminated form can occur in immunocompromised patients. Given that the diagnosis of acute Toxoplasma infection, as opposed to latent disease, relies on finding direct evidence of T. gondii infection in tissue, pathologic examination is critical. There have only been a few reports describing the cytomorphology of Toxoplasma in exfoliative cytology, and no reports of the findings in Thin Prep. In this report, we describe a fatal case of toxoplasmosis in a cardiac transplant patient that was diagnosed by respiratory cytopathology. Although the extracellular organisms were well visualized on the Wright‐Giemsa stained cytospin, they were only faintly seen on the Pap‐stained cytospin trapped within mucin and were not easily appreciated on the ThinPrep slides nor the H&E stained cell block sections. An immunohistochemical stain for Toxoplasma performed on the cell block was strongly positive, and an autopsy performed on the patient confirmed disseminated infection. Our case illustrates that the diagnosis of Toxoplasma in exfoliative cytology specimens can be challenging since organisms are not well visualized on ThinPrep or Pap‐stained material; therefore, Wright‐Giemsa stained material can be particularly helpful. Diagn. Cytopathol. 2012. © 2011 Wiley Periodicals, Inc.
Imidozirconocene‐Mediated Ring Cleavage of Epoxides – Evidence for Bifunctional Reactivity from DFT
Authors: Senthilnathan Dhurairajan , Venuvanalingam Ponnambalam 
Published: May 2011

AbstractThe ring cleavage of epoxides mediated by bis(cyclopentadienyl)(tert‐butylimido)zirconium (Cp2Zr=N–tBu)(THF) has been investigated using DFT calculations with a view to understand the mechanism of epoxide ring cleavage and the role of the imidozirconocene complex. Two types of epoxides have been chosen; some with and some without accessible β‐hydrogen atoms. Epoxides without accessible β‐hydrogen atoms undergo only insertion, whereas those with undergo both insertion and elimination. Although insertion is found to follow a zwitterionic mechanism, the elimination passes through a concerted intramolecular hydrogen transfer step. The role of the imidozirconocene complex has been elucidated by EDA and NBO analysis, which show that the vacant 1a1molecular orbital of the Lewis acidic metal center of Cp2Zr=N–tBu fragment initiates the reaction as a Lewis acidic center and the Lewis basic imido nitrogen atom of the Cp2Zr=N–tBu fragment completes the reaction. The coordinate to covalent bond conversion and the involvement of the 1a1and 2a1molecular orbitals of the Cp2Zr=N–tBu fragment in the reaction have been examined. The formation of a five‐membered metallacycle in the insertion and the alkoxy allyl product in the elimination predicted by calculations concur with experimental observations. Topological analysis has been carried out to further elucidate the mechanism and to reveal the bifunctional reactivity of imidozirconocene in epoxide ring opening reactions.
Synthesis, Characterization and Catalytic Application of Iron Complexes Modified by Monodentate Phosphane Ligands
Authors: Haberberger Michael , Irran Elisabeth , Enthaler Stephan 
Published: May 2011

AbstractIn the present study, the properties of new monodentate phosphane ligands with a N,N‐diphenyl‐1H‐pyrrol‐1‐amine moiety have been investigated. The ligands are easily accessible by lithiation of N,N‐diphenyl‐1H‐pyrrol‐1‐amine in the 2‐position and by quenching with phosphane chlorides (2: R = tBu, 3: R = Ph). After characterization of the ligands, their coordination to iron carbonyls has been studied. The ligands coordinate through the phosphorus in a monodentate fashion to the iron to realize complexes with the (L)Fe(CO)4 motif. Initial catalytic experiments have been performed; the iron‐catalyzed reduction of alkynes to alkenes with excellent selectivities to the corresponding alkenes has been achieved.
Determination of the adulteration of butter
Authors: Derewiaka Dorota , Sosińska Ewa , Obiedziński Mieczysław , Krogulec Aleksandra , Czaplicki Sylwester 
Published: May 2011

AbstractThe adulteration of butter is a serious problem due to economic advantages taken by replacing expensive milk fat with cheaper oil without informing the customers. The authentication of milk fat methods include analysis of bulk components, especially triacylglycerols, fatty acids, sterols and tocopherols. Fatty acid and sterol composition was analysed by using GC‐MS. TAG and tocopherol profiles were examined by HPLC with diode array (DAD) and fluorescence detectors (FLDs). In addition, identification of selected TAG of butter fat was conducted by LC‐atmospheric pressure chemical ionisation (APCI)/MS technique. The lipid composition of 16 different butters available on Polish market were investigated. The cholesterol content in butter fat ranged from 176.8 to 264.8 mg/100 g of fat and in two samples of milk fat β‐sitosterol was found. The total saturated fatty acid (SFA) content in milk fat was 67.1–73.5%, monounsaturated fatty acid 24.5–30.5% and polyunsaturated fatty acid was 1.2–2.0%. Abnormalities in fatty acid profiles, e.g. high concentration of linoleic fatty acid, were found in two butters. These abnormalities were also determined in TAG profiles. The examination of tocopherols in butter fat confirmed that two products were adulterated by the addition of plant oils because they contained δ‐tocopherol which is typical for plant origin foodstuffs. The methods described are useful for investigating milk fat adulterations, and the most efficient are analysis of sterols and tocopherols composition.Practical applications: The described methods are useful for investigating adulteration of milk fat. Traditional strategies rely on examination of fatty acids methyl esters and TAG; these methods have some disadvantages. Due to the variability of fatty acid composition of milk fat and because TAG analysis is complex and time consuming, FA analysis is not an efficient approach for butter authentication. The most efficient method for butter authentication is qualitative and quantitative analysis of sterols and tocopherols. This analysis will determine if components of plant origin were used for butter production.
Chiral Thiourea‐Catalyzed Asymmetric Michael Addition of β‐Oxo Phosphonate to Nitro Olefins: Convenient Synthesis of Optically Active β‐Oxo Phosphonates
Authors: Hu Kuang , Liu Tao , Lu A. D. , Liu Yunfeng , Wang Youming , Wu Guiping , Zhou Zhenghong , Tang Chuchi 
Published: May 2011

Abstractβ‐Oxo phosphonates have been proven to be alternative Michael donors in Michael addition reactions to nitro olefins in the presence of cinchonine‐based bifunctional thiourea, affording a direct and atom‐economic approach to the efficient construction of synthetically and biologically valuable chiral acyclic α‐substituted β‐oxo phosphonates with high levels of enantioselectivity (up to 98 % ee).