bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative proteomics of a lycopene‐accumulating mutant reveals the important role of oxidative stress on carotenogenesis in sweet orange (Citrus sinensis [L.] osbeck)
Authors: Pan Zhiyong , Liu Qing , Yun Ze , Guan Rui , Zeng Wenfang , Xu Qiang , Deng Xiuxin 
Published: October 2009

AbstractA spontaneous sweet orange (Citrus sinenesis [L.] Osbeck) mutant ‘Hong Anliu’ is of high value due to lycopene accumulation in the pulp. In this study, we analyzed the proteomic alterations in the pulp of ‘Hong Anliu’ versus its wild type (WT) at four maturing stages by using 2‐DE combined with MALDI‐TOF‐TOF MS. Among the 74 differentially expressed proteins identified, the majority are predicted to be involved in stress response, carbohydrate/energy metabolism and regulation, or protein fate, modification and degradation. Particularly, expression levels of six anti‐oxidative enzymes were altered by the mutation; and assays of their respective enzymatic activities indicated an enhanced level of oxidative stress in ‘Hong Anliu’, implying a regulatory role of oxidative stress on carotenogenesis. This conclusion was further confirmed by our observation that treatment of fruit pulps with tert‐butylhydroperoxide (a ROS progenitor) induced lycopene accumulation in ‘Hong Anliu’ only. Gene expression showed that genes predicted to function upstream of lycopene biosynthesis were generally upregulated in juice sacs, but downregulated in segment membranes in both ‘Hong Anliu’ and its WT. The result suggests an important role of post‐transcriptional regulation on carotenogenesis since lycopene was induced in ‘Hong Anliu’ but not WT. The result also implies that carotenogenesis in juice sacs and segment membranes of citrus fruits may be regulated by different mechanisms.
The PSI semantic validator: A framework to check MIAPE compliance of proteomics data
Authors: Montecchi‐Palazzi Luisa , Kerrien Samuel , Reisinger Florian , Aranda Bruno , Jones Andrew R. , Martens Lennart , Hermjakob Henning 
Published: October 2009

AbstractThe Human Proteome Organization's Proteomics Standards Initiative (PSI) promotes the development of exchange standards to improve data integration and interoperability. PSI specifies the suitable level of detail required when reporting a proteomics experiment (via the Minimum Information About a Proteomics Experiment), and provides extensible markup language (XML) exchange formats and dedicated controlled vocabularies (CVs) that must be combined to generate a standard compliant document. The framework presented here tackles the issue of checking that experimental data reported using a specific format, CVs and public bio‐ontologies (e.g. Gene Ontology, NCBI taxonomy) are compliant with the Minimum Information About a Proteomics Experiment recommendations. The semantic validator not only checks the XML syntax but it also enforces rules regarding the use of an ontology class or CV terms by checking that the terms exist in the resource and that they are used in the correct location of a document. Moreover, this framework is extremely fast, even on sizable data files, and flexible, as it can be adapted to any standard by customizing the parameters it requires: an XML Schema Definition, one or more CVs or ontologies, and a mapping file describing in a formal way how the semantic resources and the format are interrelated. As such, the validator provides a general solution to the common problem in data exchange: how to validate the correct usage of a data standard beyond simple XML Schema Definition validation. The framework source code and its various applications can be found at http://psidev.info/validator.
Relation between pH, structure, and absorption spectrum of Cerulean: A study by molecular dynamics and TD DFT calculations
Authors: Vallverdu Germain , Demachy Isabelle , Mérola Fabienne , Pasquier Hélène , Ridard Jacqueline , Lévy Bernard 
Published: October 2009

AbstractMolecular dynamics (MD) and quantum mechanical calculations of the Cerulean green fluorescent protein (a variant of enhanced cyan fluorescent protein ECFP) at pH 5.0 and 8.0 are presented, addressing two questions arising from experimental results (Malo et al., Biochemistry 2007;46:9865–9873): the origin of the blue shift of absorption spectrum when the pH is decreased from 8.0 to 5.0, and the lateral chain orientation of the key residue Asp148. We demonstrate that the blue shift is reproduced assuming that a rotation around the single bond of the exocyclic ring of the chromophore takes place when the pH changes from 5.0 to 8.0. We find that Asp148 is protonated and inside the barrel at pH 5.0 in agreement with crystallographic data. However, the hydrogen bond pattern of Asp148 is different in simulations of the solvated protein and in the crystal structure. This difference is explained by a partial closing of the cleft between strands 6 and 7 in MD simulations. This study provides also a structure at pH 8.0: the Asp148 carboxylate group is exposed to the solvent and the chromophore is stabilized in the trans conformation by a tighter hydrogen bond network. This work gives some insight into the relationship between the pH and the chromophore conformation and suggests an interpretation of the very similar fluorescent properties of ECFP and ECFP/H148D. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Computational design of second‐site suppressor mutations at protein–protein interfaces
Authors: Sammond Deanne W. , Eletr Ziad M. , Purbeck Carrie , Kuhlman Brian 
Published: October 2009

AbstractThe importance of a protein–protein interaction to a signaling pathway can be established by showing that amino acid mutations that weaken the interaction disrupt signaling, and that additional mutations that rescue the interaction recover signaling. Identifying rescue mutations, often referred to as second‐site suppressor mutations, controls against scenarios in which the initial deleterious mutation inactivates the protein or disrupts alternative protein–protein interactions. Here, we test a structure‐based protocol for identifying second‐site suppressor mutations that is based on a strategy previously described by Kortemme and Baker. The molecular modeling software Rosetta is used to scan an interface for point mutations that are predicted to weaken binding but can be rescued by mutations on the partner protein. The protocol typically identifies three types of specificity switches: knob‐in‐to‐hole redesigns, switching hydrophobic interactions to hydrogen bond interactions, and replacing polar interactions with nonpolar interactions. Computational predictions were tested with two separate protein complexes; the G‐protein Gαi1 bound to the RGS14 GoLoco motif, and UbcH7 bound to the ubiquitin ligase E6AP. Eight designs were experimentally tested. Swapping a buried hydrophobic residue with a polar residue dramatically weakened binding affinities. In none of these cases were we able to identify compensating mutations that returned binding to wild‐type affinity, highlighting the challenges inherent in designing buried hydrogen bond networks. The strongest specificity switches were a knob‐in‐to‐hole design (20‐fold) and the replacement of a charge–charge interaction with nonpolar interactions (55‐fold). In two cases, specificity was further tuned by including mutations distant from the initial design. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Cooperative nature of gating transitions in K+ channels as seen from dynamic importance sampling calculations
Authors: Denning Elizabeth J. , Woolf Thomas B. 
Published: October 2009

AbstractThe growing dataset of K+ channel x‐ray structures provides an excellent opportunity to begin a detailed molecular understanding of voltage‐dependent gating. These structures, while differing in sequence, represent either a stable open or closed state. However, an understanding of the molecular details of gating will require models for the transitions and experimentally testable predictions for the gating transition. To explore these ideas, we apply dynamic importance sampling to a set of homology models for the molecular conformations of K+ channels for four different sets of sequences and eight different states. In our results, we highlight the importance of particular residues upstream from the Pro‐Val‐Pro (PVP) region to the gating transition. This supports growing evidence that the PVP region is important for influencing the flexibility of the S6 helix and thus the opening of the gating domain. The results further suggest how gating on the molecular level depends on intra‐subunit motions to influence the cooperative behavior of all four subunits of the K+ channel. We hypothesize that the gating process occurs in steps: first sidechain movement, then inter‐S5‐S6 subunit motions, and lastly the large‐scale domain rearrangements. Proteins 2010. © 2009 Wiley‐Liss, Inc.
MUFOLD: A new solution for protein 3D structure prediction
Authors: Zhang Jingfen , Wang Qingguo , Barz Bogdan , He Zhiquan , Kosztin Ioan , Shang Yi , Xu Dong 
Published: October 2009

AbstractThere have been steady improvements in protein structure prediction during the past 2 decades. However, current methods are still far from consistently predicting structural models accurately with computing power accessible to common users. Toward achieving more accurate and efficient structure prediction, we developed a number of novel methods and integrated them into a software package, MUFOLD. First, a systematic protocol was developed to identify useful templates and fragments from Protein Data Bank for a given target protein. Then, an efficient process was applied for iterative coarse‐grain model generation and evaluation at the Cα or backbone level. In this process, we construct models using interresidue spatial restraints derived from alignments by multidimensional scaling, evaluate and select models through clustering and static scoring functions, and iteratively improve the selected models by integrating spatial restraints and previous models. Finally, the full‐atom models were evaluated using molecular dynamics simulations based on structural changes under simulated heating. We have continuously improved the performance of MUFOLD by using a benchmark of 200 proteins from the Astral database, where no template with >25% sequence identity to any target protein is included. The average root‐mean‐square deviation of the best models from the native structures is 4.28 Å, which shows significant and systematic improvement over our previous methods. The computing time of MUFOLD is much shorter than many other tools, such as Rosetta. MUFOLD demonstrated some success in the 2008 community‐wide experiment for protein structure prediction CASP8. Proteins 2010. © 2009 Wiley‐Liss, Inc.
The effect of calcium on the conformation of cobalamin transporter BtuB
Authors: Luan Binquan , Carr Rogan , Caffrey Martin , Aksimentiev Aleksei 
Published: October 2009

AbstractBtuB is a β‐barrel membrane protein that facilitates transport of cobalamin (vitamin B12) from the extracellular medium across the outer membrane of Escherichia coli. It is thought that binding of B12 to BtuB alters the conformation of its periplasm‐exposed N‐terminal residues (the TonB box), which enables subsequent binding of a TonB protein and leads to eventual uptake of B12 into the cytoplasm. Structural studies determined the location of the B12 binding site at the top of the BtuB's β‐barrel, surrounded by extracellular loops. However, the structure of the loops was found to depend on the method used to obtain the protein crystals, which—among other factors—differed in calcium concentration. Experimentally, calcium concentration was found to modulate the binding of the B12 substrate to BtuB. In this study, we investigate the effect of calcium ions on the conformation of the extracellular loops of BtuB and their possible role in B12 binding. Using all‐atom molecular dynamics, we simulate conformational fluctuations of several X‐ray structures of BtuB in the presence and absence of calcium ions. These simulations demonstrate that calcium ions can stabilize the conformation of loops 3–4, 5–6, and 15–16, and thereby prevent occlusion of the binding site. Furthermore, binding of calcium ions to extracellular loops of BtuB was found to enhance correlated motions in the BtuB structure, which is expected to promote signal transduction. Finally, we characterize conformation dynamics of the TonB box in different X‐ray structures and find an interesting correlation between the stability of the TonB box structure and calcium binding. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Multiscale simulations of protein landscapes: Using coarse‐grained models as reference potentials to full explicit models
Authors: Messer Benjamin M. , Roca Maite , Chu Zhen T. , Vicatos Spyridon , Kilshtain Alexandra Vardi , Warshel Arieh 
Published: October 2009

AbstractEvaluating the free‐energy landscape of proteins and the corresponding functional aspects presents a major challenge for computer simulation approaches. This challenge is due to the complexity of the landscape and the enormous computer time needed for converging simulations. The use of simplified coarse‐grained (CG) folding models offers an effective way of sampling the landscape but such a treatment, however, may not give the correct description of the effect of the actual protein residues. A general way around this problem that has been put forward in our early work (Fan et al., Theor Chem Acc 1999;103:77–80) uses the CG model as a reference potential for free‐energy calculations of different properties of the explicit model. This method is refined and extended here, focusing on improving the electrostatic treatment and on demonstrating key applications. These applications include: evaluation of changes of folding energy upon mutations, calculations of transition‐states binding free energies (which are crucial for rational enzyme design), evaluations of catalytic landscape, and evaluations of the time‐dependent responses to pH changes. Furthermore, the general potential of our approach in overcoming major challenges in studies of structure function correlation in proteins is discussed. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Study on secondary phase precipitate behavior in Zircaloy‐2 by positron annihilation spectroscopy
Authors: Mulki S. , Pujari P. K. , Srivastava D. , Samajdar I. , Dey G. K. , Sharma S. 
Published: October 2009

AbstractIt is well established that in Zr alloys, secondary phase precipitates (SPP) have a major influence on the corrosion and mechanical properties. Thus it is important to understand the kinetics and growth of precipitates under thermal treatments. In this study, secondary phase precipitates were generated by suitable heat treatment at 800 °C and 840 °C for different duration (1‐1440 minutes). Positron lifetime spectroscopy and Doppler broadening measurements were carried out to examine the nucleation and growth aspects of the precipitates. The variation in lifetime and S‐parameter were seen to be consistent. From the S‐W curve it is seen that the defects associated with precipitation at 800 °C and 840 °C are different. Possible mechanism for precipitation of SPP's has been proposed based on the positron annihilation data. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The responses to stress questionnaire: construct validity and prediction of depressive and social anxiety symptoms in a sample of Chinese adolescents
Authors: Xiao Jing , Yao Shuqiao , Zhu Xiongzhao , Zhang Chenchen , Auerbach Randy P. , McWhinnie Chad M. , Abela John R. Z. 
Published: October 2009

AbstractThe objective of the current study was to develop a Chinese version of the Responses to Stress Questionnaire (RSQ‐C) and to evaluate its reliability and validity. The original version of the RSQ was back‐translated into Chinese and administered to a sample of students recruited from two middle schools in Hunan, China. The final sample consisted of 1068 adolescents (49.9% males and 50.1% females). Participants' ages ranged from 14 to 20 (M = 16.47 years, standard deviation = 1.02). The RSQ‐C exhibited moderate internal consistency (Cronbach's alpha was 0.87), and test–retest reliability (intraclass correlation coefficients was 0.82 over a 1‐month interval). Results of confirmatory factor analyses indicated that the fit of a three‐factor model of voluntary coping and a separate two‐factor model of involuntary coping. With regard to predictive validity, the results of multiple regression analyses suggest that the high levels of Disengagement Coping and low levels of Primary Control Engagement Coping were significant predictors of depressive symptomology. Additionally, high levels of Involuntary Engagement and low levels of Primary Control Engagement Coping predicted higher levels of social anxiety symptoms. Copyright ? 2009 John Wiley & Sons, Ltd.
Surgical Outcomes Auditing Systems in Humanitarian Organizations
Authors: Bermudez Luis , Carter Victoria , Magee William , Sherman Randy , Ayala Ruben 
Published: October 2009

AbstractBackgroundOperation Smile is a humanitarian volunteer‐based organization that provides cleft care around the world. Successful primary surgery is the key to improving the quality of life of patients with oral clefts. A cleft surgery outcomes database and evaluation system has been developed and implemented.MethodsDuring Operation Smile’s “World Journey of Smiles” in November 2007, a total of 4100 patients were operated on during a 10‐day period at 40 simultaneous missions in 25 countries. Photographs taken before surgery, right after surgery, and at the follow‐up consultations were entered in a database and used as media to evaluate surgical outcomes objectively by independent unbiased evaluators. Data about complications collected during the postoperative consultations were also entered.ResultsA postoperative consultation, 6 months to 1 year after surgery was conducted at 24 sites, 19 of which sent back postoperative images; and most returned postoperative examination forms. At those 19 sites, 703 of 1917 patients returned for a 6‐ to 9‐month postoperative visit, for a 36.67% return rate. After matching before and after pictures, 562 patients were able to be entered into the database, allowing 580 procedures to be evaluated. Feedback reports have been sent to 134 volunteer surgeons around the world. Results were compared among sites and locations; and the places where future actions were needed to improve the quality of surgery were identified.ConclusionsThe current outcomes evaluation system has proven beneficial in tracking patient outcomes, auditing surgical performance, and providing feedback to surgeons and other team members. Challenges are discussed.
Reexcision of Soft Tissue Sarcoma: Sufficient Local Control but Increased Rate of Metastasis
Authors: Rehders A. , Stoecklein N. H. , Poremba C. , Alexander A. , Knoefel W. T. , Peiper M. 
Published: October 2009

AbstractBackgroundAssuming a benign tumor, soft tissue sarcomas are often treated by inadequate resection. The concept of reexcision in these patients is still under debate. Therefore, it was our goal to evaluate the results of this treatment with particular respect to residual tumor.MethodsDuring a 14‐year period, a total of 143 patients were referred to our institution after unplanned excision. Reexcision was performed in 139 patients. The assessed endpoints were local recurrence‐free survival, distant metastasis‐free survival, and tumor‐related mortality. Univariate and multivariate analyses were performed using a log‐rank test and Cox’s proportional‐hazard models.ResultsOver a median observation period of 109 months, local recurrence appeared in 18 patients (12%) and distant metastasis in 46 patients (33%). Residual tumor was detected in 43 patients (31%) and was significantly associated with reduced relapse‐free and overall survival. Local recurrence, however, was not affected.ConclusionsDespite an incomplete initial resection, reexcision enables local control similar to that in patients without residual tumor. Still, these patients have a worse prognosis owing to an increased rate of distant metastasis; therefore, patients with soft tissue masses of unknown identity should be transferred to centers that specialize in treating sarcomas for adequate initial resection.
A Social Ecological Conceptual Framework for Understanding Adolescent Health Literacy in the Health Education Classroom
Authors: Wharf Higgins Joan , Begoray Deborah , MacDonald Marjorie 
Published: October 2009

AbstractWith the rising concern over chronic health conditions and their prevention and management, health literacy is emerging as an important public health issue. As with the development of other forms of literacy, the ability for students to be able to access, understand, evaluate and communicate health information is a skill best developed during their years of public schooling. Health education curricula offer one approach to develop health literacy, yet little is known about its influence on neither students nor their experiences within an educational context. In this article, we describe our experience applying a social ecological model to investigating the implementation of a health education curriculum in four high schools in British Columbia, Canada. We used the model to guide a conceptual understanding of health literacy, develop research questions, select data collection strategies, and interpret the findings. Reflections and recommendations for using the model are offered.
Increases in Tolerance Within Naturalistic, Intentional Communities: A Randomized, Longitudinal Examination
Authors: Olson Brad , Jason Leonard A. , Davidson Michelle , Ferrari Joseph R. 
Published: October 2009

AbstractThe authors examine differential changes in values of tolerance among 150 participants discharged from inpatient treatment centers, and randomly assigned to either a self‐help‐based, communal living setting (i.e., Oxford House), or usual aftercare. Participants were interviewed every 6 months for a 24‐month period. Hierarchical linear modeling (HLM) was used to examine the effect of condition (therapeutic communal living versus usual aftercare) on wave trajectories of tolerance (i.e., universality/diversity scores). Over time, residents of the communal living model demonstrated significantly greater values of tolerance than usual aftercare participants. Communal living participants who resided in the house for over 6 months showed the most substantial increases in tolerance. Results support the notion that communal living residents may develop more tolerant attitudes by striving toward superordinate community goals (objectives held by (a) the whole group and (b) which individual members could not achieve alone).
Snap-Through Instability of Graphene on Substrates
Authors: Li Teng , Zhang Zhao 
Published: October 2009

Abstract
We determine the graphene morphology regulated by substrates with herringbone and checkerboard surface corrugations. As the graphene–substrate interfacial bonding energy and the substrate surface roughness vary, the graphene morphology snaps between two distinct states: (1) closely conforming to the substrate and (2) remaining nearly flat on the substrate. Since the graphene morphology is strongly tied to the electronic properties of graphene, such a snap-through instability of graphene morphology can lead to desirable graphene electronic properties that could potentially enable graphene-based functional electronic components (e.g. nano-switches).