bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular dynamic simulation studies on the effect of one residue chain staggering on the structure and stability of heterotrimeric collagen‐like peptides with interruption
Authors: Singam Ettayapuram Ramaprasad Azhagiya , Balamurugan Kanagasabai , Gopalakrishnan Ravimohan , Subramanian Sundar Raman , Subramanian Venkatesan , Ramasami Thirumalachari 
Published: May 2012

AbstractA systematic molecular dynamics (MD) simulation has been carried out on collagen‐like peptides with different combinations of interruptions in the Gly–XAA–YAA repeats. Although experimental studies have been carried out to elucidate the structural consequences of homotrimeric collagen‐like peptides, this is the first report on the structural effect on the heterotrimeric models with G4G and G1G breaks present simultaneously in the constituent chains with difference in one residue chain staggering. The results reveal that the axial registry of the interrupted region changes significantly from that of conventional triple helical peptide without interruption. Further, results from MD simulations show the formation of a kink in the interrupted region of the triple‐helical peptides. The conformational analysis reveals that the interruption in the Gly–XAA–YAA pattern in these peptides induces β‐strand conformation in triple helical peptides. The conventional hydrogen bonds in the interrupted triad are affected and new nonconventional H‐bonds are formed in the triple helical structure, and as a result interrupted region becomes locally fragile. MM‐PBSA calculations on the different systems clearly suggest that the binding affinity varies marginally due to one residue staggering. However, it is found from the structural parameters that hydrogen‐bonding pattern differs significantly due to the difference in the staggering of chains. © 2012 Wiley Periodicals, Inc. Biopolymers 97:847–863, 2012.
Dissimilatory nitrate reduction by Pseudomonas alcaliphila with an electrode as the sole electron donor
Authors: Su Wentao , Zhang Lixia , Li Daping , Zhan Guoqiang , Qian Junwei , Tao Yong 
Published: May 2012

AbstractDenitrification and dissimilatory nitrate reduction to ammonium (DNRA) were considered two alternative pathways of dissimilatory nitrate reduction. In this study, we firstly reported that both denitrification and DNRA occurred in Pseudomonas alcaliphila strain MBR with an electrode as the sole electron donor in a double chamber bio‐electrochemical system (BES). The initial concentration of nitrate appeared as a factor determining the type of nitrate reduction with electrode as the sole electron donor at the same potential (−500 mV). As the initial concentration of nitrate increased, the fraction of nitrate reduced through denitrification also increased. While nitrite (1.38 ± 0.04 mM) was used as electron acceptor instead of nitrate, the electrons recovery via DNRA and denitrification were 43.06 ± 1.02% and 50.51 ± 1.37%, respectively. The electrochemical activities and surface topography of the working electrode catalyzed by strain MBR were evaluated by cyclic voltammetry and scanning electron microscopy. The results suggested that cells of strain MBR were adhered to the electrode, playing the role of electron transfer media for nitrate and nitrite reduction. Thus, for the first time, the results that DNRA and denitrification occurred simultaneously were confirmed by powering the strain with electricity. The study further expanded the range of metabolic reactions and had potential value for the recognization of dissimilatory nitrate reduction in various ecosystems. Biotechnol. Bioeng. 2012; 109: 2904–2910. © 2012 Wiley Periodicals, Inc.
Targeted codon optimization improves translational fidelity for an Fc fusion protein
Authors: Hutterer Katariina M. , Zhang Zhongqi , Michaels Mark Leo , Belouski Ed , Hong Robert W. , Shah Bhavana , Berge Mark , Barkhordarian Hedieh , Le Eleanor , Smith Steve , Winters Dwight , Abroson Frank , Hecht Randy , Liu Jennifer 
Published: May 2012

AbstractHigh levels of translational errors, both truncation and misincorporation in an Fc‐fusion protein were observed. Here, we demonstrate the impact of several commercially available codon optimization services, and compare to a targeted strategy. Using the targeted strategy, only codons known to have translational errors are modified. For an Fc‐fusion protein expressed in Escherichia coli, the targeted strategy, in combination with appropriate fermentation conditions, virtually eliminated misincorporation (proteins produced with a wrong amino acid sequence), and reduced the level of truncation. The use of full optimization using commercially available strategies reduced the initial errors, but introduced different misincorporations. However, truncation was higher using the targeted strategy than for most of the full optimization strategies. This targeted approach, along with monitoring of translation fidelity and careful attention to fermentation conditions is key to minimizing translational error and ensuring high‐quality expression. These findings should be useful for other biopharmaceutical products, as well as any other transgenic constructs where protein quality is important. Biotechnol. Bioeng. 2012; 109: 2770–2777. © 2012 Wiley Periodicals, Inc.
‘Artery-first’ approaches to pancreatoduodenectomy
Authors: Sanjay P , Takaori K , Govil S , Shrikhande S V , Windsor J A 
Published: May 2012

Abstract

Background
The technique of pancreatoduodenectomy (PD) has evolved. Previously, non-resectability was determined by involvement of the portal vein–superior mesenteric vein. Because venous resection can be achieved safely and with greater awareness of the prognostic significance of the status of the posteromedial resection margin, non-resectability is now determined by involvement of the superior mesenteric artery (SMA). This change, with a need for early determination of resectability before an irreversible step, has promoted the development of an ‘artery-first’ approach. The aim of this study was to review, and illustrate, this approach.

Methods
An electronic search was performed on MEDLINE, Embase and PubMed databases from 1960 to 2011 using both medical subject headings and truncated word searches to identify all published articles that related to this topic.

Results
The search revealed six different surgical approaches that can be considered as ‘artery first’. These involved approaching the SMA from the retroperitoneum (posterior approach), the uncinate process (medial uncinate approach), the infracolic region medial to the duodenojejunal flexure (inferior infracolic or mesenteric approach), the infracolic retroperitoneum lateral to the duodenojenunal flexure (left posterior approach), the supracolic region (inferior supracolic approach) and through the lesser sac (superior approach).

Conclusion
The six approaches described provide a range of options for the early determination of arterial involvement, depending on the location and size of the tumour, and before the ‘point of no return’. Whether these approaches will achieve an increase in the proportion of patients with negative margins, improve locoregional control and increase long-term survival has yet to be determined.
Production of Organic Fine‐Crystalline Particles by Using the Liquid‐Liquid Interface in an Emulsion
Authors: Takiyama H. , Ito K. 
Published: May 2012

AbstractThe method of anti‐solvent crystallization poses problems due to high local fluctuations in supersaturation affecting the quality of the generated crystals. In order to reduce the local fluctuations in supersaturation and to achieve homogeneous crystallization fields, the utilization of a liquid‐liquid interface in an emulsion is discussed. The purpose of this study was to establish the operating conditions of crystallization in order to produce fine crystals with the desired qualities by anti‐solvent crystallization in an emulsion. A quaternary system of taurine/water (original solvent)/hexane (anti‐solvent)/ethanol (coupled solvent) was used. As the experimental result, micro‐sized taurine crystals were obtained, and the operation conditions to obtain the desired crystal shape were clarified by utilizing the proposed quaternary phase diagram.
Crystal‐Packing Trends for a Series of 6,9,12,15,18‐Pentaaryl‐1‐hydro[60]fullerenes
Authors: Kennedy Robert D. , Halim Merissa , Khan Saeed I. , Schwartz Benjamin J. , Tolbert Sarah H. , Rubin Yves 
Published: May 2012

AbstractThe relationship between the size of the substituents of aryl groups in a series of fifteen 6,9,12,15,18‐pentaaryl‐1‐hydro[60]fullerenes and the solid‐state structures and packing motifs of these compounds has been analyzed. Pentaarylfullerenes have a characteristic “badminton shuttlecock” shape that causes several derivatives to crystallize into columnar stacks. However, many pentaarylfullerenes form non‐stacked structures with, for example, dimeric, layered, diamondoid, or feather‐in‐cavity relationships between molecules. Computational modeling gave a qualitative estimate of the best shape match between the ball and socket surfaces of each pentaarylfullerene. The best match was for pentaarylfullerenes with large, spherically shapedpara‐substituents on the aryl groups. The series of pentaarylfullerenes was characterized by single‐crystal X‐ray diffraction. A total of 34 crystal structures were obtained as various solvates and were categorized by their packing motifs.
Controllable Deposition of a Platinum Nanoparticle Ensemble on a Polyaniline/Graphene Hybrid as a Novel Electrode Material for Electrochemical Sensing
Authors: Qiu Jian‐Ding , Shi Ling , Liang Ru‐Ping , Wang Guo‐Chong , Xia Xing‐Hua 
Published: May 2012

AbstractWe demonstrate for the first time an interfacial polymerization method for the synthesis of high‐quality polyaniline‐modified graphene nanosheets (PANI/GNs), which represents a novel type of graphene/polymer heterostructure. The interfacial polymerization at a liquid–liquid interface allows PANI to grow uniformly on the surface of the GNs. An ultra‐high loading of Pt nanoparticles was then controllably deposited on the surface of the PANI/GNs to form a Pt/PANI/GNs hybrid. The obtained composites were characterized by scanning electron microscopy, transmission electron microscopy, energy‐dispersive spectrometry, X‐ray diffraction, X‐ray photoelectron spectroscopy, and thermogravimetric analysis. The Pt/PANI/GNs hybrid shows excellent electrocatalytic activity toward methanol oxidation and oxygen reduction. H2O2 and glucose were used as two representative analytes to demonstrate the sensing performance of a Pt/PANI/GNs‐modified electrode. It is found that this sensing element shows high sensitivity and a low detection limit for H2O2 and glucose. The results demonstrate that the Pt/PANI/GNs hybrid may be an attractive and advanced electrode material with potential applications in the construction of electrochemical sensors and biosensors.
Facile Fabrication of a Graphene‐based Electrochemical Biosensor for Glucose Detection
Authors: Zhang Yanqin , Fan Youjun , Wang Shanshan , Tan Yiliang , Shen Xingcan , Shi Zujin 
Published: May 2012

AbstractA simple and effective glucose biosensor based on immobilization of glucose oxidase (GOD) in graphene (GR)/Nafion film was constructed. The results indicated that the immobilized GOD can maintain its native structure and bioactivity, and the GR/Nafion film provides a favorable microenvironment for GOD immobilization and promotes the direct electron transfer between the electrode substrate and the redox center of GOD. The electrode reaction of the immobilized GOD shows a reversible and surface‐controlled process with the large electron transfer rate constant (ks) of 3.42±0.08 s−1. Based on the oxygen consumption during the oxidation process of glucose catalyzed by the immobilized GOD, the as‐prepared GOD/GR/Nafion/GCE electrode exhibits a linear range from 0.5 to 14 mmol·L−1 with a detection limit of 0.03 mmol·L−1. Moreover, it displays a good reproducibility and long‐term stability.
Interfacial Water Structure in Langmuir Monolayer and Gibbs Layer Probed by Sum Frequency Generation Vibrational Spectroscopy
Authors: Zhang Zhen , Guo Yuan 
Published: May 2012

AbstractLangmuir monolayer and Gibbs layer exhibit surface‐active properties and it can be used as simple model systems to investigate the physicochemical properties of biological membranes. In this report, we presented the OH stretching vibration of H2O in the 4′′‐n‐pentyl‐4‐cyano‐p‐terphenyl (5CT), nonadecanenitrile (C18CN) Langmuir monolayer and compared them with CH3CN Gibbs layer at the air/water interface with polarization SFG‐VS. This study demonstrated that the hydrogen bond network is different in the Langmuir monolayer of 5CT, C18CN from CH3CN Gibbs layer at the air/water interface which showed two different water structures on the different surface layer. The results provided a deeper insight into understanding the hydrogen bond on the interfaces.
A Study of Interaction between Flavonoids and the Parallel Quadruplex Structure [d(TGGGGT)]4 by Electrospray Ionization Mass Spectrometry
Authors: Xu Niusheng , Yang Hongmei , Cui Meng , Song Fengrui , Liu Zhiqiang , Liu Shuying 
Published: May 2012

AbstractIn this study, electrospray ionization mass spectrometry (ESI‐MS) was used to investigate interaction of 21 flavonoids (10 aglycones and 11 glycosides) with the parallel quadruplex structure [d(TGGGGT)]4. Relative binding affinities of flavonoids toward [d(TGGGGT)]4 were estimated based on the fraction of bound DNA. It was found that [d(TGGGGT)]4 showed a binding preference to the flavonoid glycosides over flavonoid aglycones. It was deduced that glycosylation played a key role for the [d(TGGGGT)]4‐binding properties of flavonoid glycosides. Upon collision‐induced dissociation, complexes of flavonoid/[d(TGGGGT)]4 underwent the loss of flavonoids, suggesting an end‐stacking binding mode. The current work demonstrates that ESI‐MS is a powerful tool in the study of interaction between drugs and nucleic acids.
Synthsis of 4‐Piperidones via Multicomponent Double Mannich Reaction Catalyzed by I2
Authors: Jia Xiaodong , Chen Xiangning , Huo Congde , Peng Fangfang , Qing Chang , Wang Xicun 
Published: May 2012

AbstractA multicomponent double Mannich reaction of amines, aldehydes and ketones was efficiently catalyzed by molecular iodine, producing a series of 4‐piperidones in a stereoselective way. A variety of amines, aldehydes and ketones were tolerated in this tandem process, including those with labile functinal groups. Further investigation of the reaction between alkyl‐imines and ketones showed that imines from amines and ketones were formed in situ and isomerized to enamine in the presence of molecular iodine to accelerate the corresponding Mannich addition.
NBS‐Promoted Sulfenylation of Sulfinates with Disulfides Leading to Unsymmetrical or Symmetrical Thiosulfonates
Authors: Liang Gaigai , Liu Miaochang , Chen Jiuxi , Ding Jinchang , Gao Wenxia , Wu Huayue 
Published: May 2012

AbstractA highly practical method to access unsymmetrical and symmetrical thiosulfonates in moderate to excellent yields has been developed through NBS‐promoted sulfenylation of sulfinates with disulfides. The present process enables the use of two RS in RSSR and shows broad functional group tolerance, which represents an atom‐economical and practical procedure for the synthesis of thiosulfonates. A plausible mechanism for the role of NBS as a promoter for the cleavage of disul?des generating N‐(organothio)succinimide that then undergos facile sulenylation with sulfinates is proposed.
The Role of the Therapeutic Alliance in the Regulation of Emotion in Psychosis: An Attachment Perspective
Authors: Owens Karen Annette , Haddock Gillian , Berry Katherine 
Published: May 2012

Objectives: This article aims to explore the value of attachment theory as a framework for understanding the ways in which the staff–patient relationship is associated with different methods of regulating emotion in individuals with a diagnosis of psychosis. Method: Patient participants with a diagnosis of schizophrenia, schizoaffective disorder or psychosis not otherwise specified and mental health workers were recruited from 24‐hour rehabilitation teams. Patient participants completed questionnaires assessing emotion regulation, attachment, therapeutic alliance and symptomatology. The therapeutic alliance was also assessed from mental workers' perspective. Results: Insecure attachment was significantly associated with greater difficulties in regulating emotions. A strong therapeutic alliance was associated with fewer difficulties in regulating emotions. Conclusions: Attachment is a useful theoretical construct for understanding psychosis, with evidence for a link between a positive staff–patient relationship and enhanced emotion regulation. Clinical implications of these findings are discussed. Copyright © 2012 John Wiley & Sons, Ltd.Key Practitioner Message

The study supports a link between attachment organisation and psychosis, characterised by difficulties in emotion regulation.
A positive patient‐key worker relationship may facilitate the development of emotion regulation in this client group.
A key implication of these findings is the training of MDT staff in the implementation of attachment‐informed interventions.
The Origin of Molecular Mobility During Biomass Pyrolysis as Revealed by In situ 1H NMR Spectroscopy
Authors: Dufour Anthony , Castro‐Diaz Miguel , Brosse Nicolas , Bouroukba Mohamed , Snape Colin 
Published: May 2012

AbstractThe thermochemical conversion of lignocellulosic biomass feedstocks offers an important potential route for the production of biofuels and value‐added green chemicals. Pyrolysis is the first phenomenon involved in all biomass thermochemical processes and it controls to a major extent the product composition. The composition of pyrolysis products can be affected markedly by the extent of softening that occurs. In spite of extensive work on biomass pyrolysis, the development of fluidity during the pyrolysis of biomass has not been quantified. This paper provides the first experimental investigation of proton mobility during biomass pyrolysis by in situ 1H NMR spectroscopy. The origin of mobility is discussed for cellulose, lignin and xylan. The effect of minerals on cellulose mobility is also investigated. Interactions between polymers in the native biomass network are revealed by in situ 1H NMR analysis.
Sulforhodamine B restaining as a whole‐cell label allows visualizing one more fluorochrome and its application in assaying protein nucleocytoplasmic distribution
Authors: Han Fujun , Fan Lifei , Wang Xinsheng , Li Wei 
Published: May 2012

AbstractMultiparametric image analysis is highly preferable in revealing complicated biological processes. The multiplexing capability is demanding and is limited by spectral overlap of fluorescent dyes and the number of fluorescent channels available in an imaging platform, especially when both nuclear and cytoplasmic staining are required for the analysis. Here, we introduce a retrospective method that enables cell labeling by restaining the cells with sulforhodamine B (SRB) using a positioning‐stage equipped microscope and an automated image registration technique. Using signal transducers and activator of transcription 1 (STAT1) nuclear translocation as an example, this method was shown to be able to improve the reliability and multiplexing capability of protein distribution assays. The application of this method in a three‐fluorescent channel platform is functionally equal to a conventional four‐color assay and enables the correlation between cellular distributions of two proteins expressed at very low levels to be detected. We have demonstrated this application using STAT3 and syndecan‐1. For the first time, we found that the two proteins were correlated at both the nuclear:cytoplasmic distribution and expression levels. This experimental direction could advance our understanding as to how these molecules function. The simplicity and automation of this method makes it easily applicable into other imaging assays. Other dyes can be used in a similar way as substitutes of SRB. © 2012 International Society for Advancement of Cytometry
Bivalent response to long‐term storage in liquid‐preserved boar semen: A flow cytometric analysis
Authors: Henning Heiko , Petrunkina Anna M. , Harrison Robin A. P. , Waberski Dagmar 
Published: May 2012

AbstractThe fertility of liquid‐preserved boar semen declines during storage at 17°C, insemination trials even indicating early losses in fertilizing ability within the first 24–48 h of storage. Standard semen parameters barely reflect these changes in semen quality, and new approaches for assessment of functional changes in stored spermatozoa are needed. Capacitation, the essential prefertilization step for spermatozoa in the female genital tract, is specifically induced in vitro by bicarbonate. Therefore, we have investigated changes in responsiveness of boar spermatozoa to bicarbonate during storage. Ejaculates of 14 boars were diluted in Beltsville thawing solution, cooled to 17°C and stored for 12, 24, 72, 120, and 168 h before investigation. At each time, basic semen quality was characterized by sperm motility and viability. Subsequently, washed subsamples were incubated in variants of an in vitro fertilization (IVF) medium and assessed for kinetic changes of viability (plasma membrane integrity) and intracellular calcium concentration using flow cytometry in combination with propidium iodide and Fluo‐3. By this means, it was possible to determine specific effects of bicarbonate and calcium on sperm subpopulations over incubation time. During storage, standard semen parameters remained on a high level. However, flow cytometric analysis of sperm responses to capacitating and control media revealed two opposing effects of storage. There was a loss of response to bicarbonate in part of the live sperm population but an increasing degree of instability in the rest. Assessment of response to capacitating media by flow cytometry appears a markedly more sensitive way of monitoring sperm functionality during storage than the standard semen parameters of motility and viability. © 2012 International Society for Advancement of Cytometry