bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in the human plasma and urinary metabolome associated with acute dietary exposure to sucrose and the identification of potential biomarkers of sucrose intake
Authors: Beckmann Manfred , Joosen Annemiek M. , Clarke Michelle M. , Mugridge Owen , Frost Gary , Engel Barbara , Taillart Kathleen , Lloyd Amanda J. , Draper John , Lodge John K. 
Published: August 2015

ScopeThe intake of sucrose is of public health concern but limited information is available on the metabolic effects of short‐term exposure. Our aim was to use metabolomics to investigate the metabolic impact of acute sucrose exposure.Methods and resultsWe performed a randomized, parallel, single‐dose feeding study on healthy females (n = 90, aged 29.9 ± 4.7 years, BMI 23.3 ± 2.5 kg/m2) consuming either 0, 50, or 100 g sucrose in 500 mL water. Blood and urine samples were taken before and 24 h post sucrose intake. Urine and plasma samples underwent detailed metabolite profiling analysis using established protocols. Flow‐injection electrospray MS fingerprinting analysis showed that 3 h after intake was the most informative time point in urine and plasma and out of 120 explanatory signals, highlighted 16 major metabolite signals in urine and 25 metabolite signals in plasma that were discriminatory and correlated with sucrose intake over time. The main confirmed metabolites positively correlated with intake were sucrose, fructose, and erythronic acid, while those negatively correlating with intake included fatty acids and derivatives, acyl‐carnitines, and ketone bodies. GC‐TOF‐MS profiling analysis confirmed the fingerprinting data.ConclusionAcute exposure to sucrose identified a number of metabolites correlated with sucrose intake and several compounds attributed to metabolic fasting.
Which Factors Influence Self‐Efficacy in Patients with Chronic Inflammatory Polyarthritis?
Authors: Grønning Kjersti , Bratås Ola , Steinsbekk Aslak 
Published: August 2015

AbstractObjectivesPatients with rheumatoid arthritis (RA), psoriatic arthritis (PsA) or unspecified polyarthritis (UA) deal with several symptoms such as joint stiffness, pain, physical limitations and fatigue. Self‐efficacy is about patients’ beliefs and abilities to handle the symptoms and implications of having arthritis. Patients’ self‐efficacy is also a phenomenon that nurses may affect through patient education. Therefore, the aim of the present study was to investigate the factors that predict self‐efficacy in patients with chronic inflammatory polyarthritis.MethodsThe participants (n = 132) were recruited from St Olavs University Hospital in central Norway from 2008 to 2010, and consisted of adult patients with RA, PsA or UA. We performed secondary analyses on data collected in a randomized controlled trial studying the long‐term effects of nurse‐led patient education. We carried out bivariate and multivariate linear regression analyses. The predictor variables consisted of baseline data on demographics, disease characteristics (diagnosis, disease duration, disease activity, use of disease‐modifying anti‐rheumatic drugs, pain and tiredness) and psychological variables (well‐being, psychological distress and patient activation). The dependent variables were self‐efficacy over other symptoms and self‐efficacy over for pain after one year.ResultsThe analyses showed that female gender and patient activation predicted higher self‐efficacy over other symptoms, whereas female gender and better well‐being predicted higher self‐efficacy over pain.ConclusionTo strengthen arthritis patients’ self‐efficacy, nurses need to focus on patients’ well‐being and activation. Nurses also need to be aware of possible gender differences regarding patients’ self‐efficacy. Copyright © 2015 John Wiley & Sons, Ltd.
Optimizing testing methods and collection of reference data for differentiating critical illness polyneuropathy from critical illness MYOPATHIES
Authors: Marrero Humberto Gonzalez , Stålberg Erik V. 
Published: August 2015

ABSTRACTIntroduction: In severe acute quadriplegic myopathy in intensive care unit (ICU) patients, muscle fibers are electrically inexcitable; in critical illness polyneuropathy, the excitability remains normal. Conventional electrodiagnostic methods do not provide the means to adequately differentiate between them. In this study we aimed to further optimize the methodology for the study of critically ill ICU patients and to create a reference database in healthy controls. Methods: Different electrophysiologic protocols were tested to find sufficiently robust and reproducible techniques for clinical diagnostic applications. Results: Many parameters show large test–retest variability within the same healthy subject. Reference values have been collected and described as a basis for studies of weakness in critical illness. Conclusions: Using the ratio of neCMAP/dmCMAP (response from nerve and direct muscle stimulation), refractory period, and stimulus–response curves may optimize the electrodiagnostic differentiation of patients with critical illness myopathy from those with critical illness polyneuropathy. Muscle Nerve 53: 555–563, 2016
Weak conservation of structural features in the interfaces of homologous transient protein–protein complexes
Authors: Sudha Govindarajan , Singh Prashant , Swapna Lakshmipuram S. , Srinivasan Narayanaswamy 
Published: August 2015

AbstractResidue types at the interface of protein–protein complexes (PPCs) are known to be reasonably well conserved. However, we show, using a dataset of known 3‐D structures of homologous transient PPCs, that the 3‐D location of interfacial residues and their interaction patterns are only moderately and poorly conserved, respectively. Another surprising observation is that a residue at the interface that is conserved is not necessarily in the interface in the homolog. Such differences in homologous complexes are manifested by substitution of the residues that are spatially proximal to the conserved residue and structural differences at the interfaces as well as differences in spatial orientations of the interacting proteins. Conservation of interface location and the interaction pattern at the core of the interfaces is higher than at the periphery of the interface patch. Extents of variability of various structural features reported here for homologous transient PPCs are higher than the variation in homologous permanent homomers. Our findings suggest that straightforward extrapolation of interfacial nature and inter‐residue interaction patterns from template to target could lead to serious errors in the modeled complex structure. Understanding the evolution of interfaces provides insights to improve comparative modeling of PPC structures.
The value of protein structure classification information—Surveying the scientific literature
Authors: Fox Naomi K. , Brenner Steven E. , Chandonia John‐Marc 
Published: August 2015

ABSTRACTThe Structural Classification of Proteins (SCOP) and Class, Architecture, Topology, Homology (CATH) databases have been valuable resources for protein structure classification for over 20 years. Development of SCOP (version 1) concluded in June 2009 with SCOP 1.75. The SCOPe (SCOP–extended) database offers continued development of the classic SCOP hierarchy, adding over 33,000 structures. We have attempted to assess the impact of these two decade old resources and guide future development. To this end, we surveyed recent articles to learn how structure classification data are used. Of 571 articles published in 2012–2013 that cite SCOP, 439 actually use data from the resource. We found that the type of use was fairly evenly distributed among four top categories: A) study protein structure or evolution (27% of articles), B) train and/or benchmark algorithms (28% of articles), C) augment non‐SCOP datasets with SCOP classification (21% of articles), and D) examine the classification of one protein/a small set of proteins (22% of articles). Most articles described computational research, although 11% described purely experimental research, and a further 9% included both. We examined how CATH and SCOP were used in 158 articles that cited both databases: while some studies used only one dataset, the majority used data from both resources. Protein structure classification remains highly relevant for a diverse range of problems and settings. Proteins 2015; 83:2025–2038. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.
Educational Expansion and Intergenerational Proximity in Sweden
Authors: Chudnovskaya Margarita , Kolk Martin 
Published: August 2015

AbstractEducation is one of the most important drivers of regional migration in European countries, and educational expansion has been a major social phenomenon in the last decades. We use decomposition analysis to examine how the expansion of tertiary education has affected intergenerational distance between adult children and their parents in Sweden. We use administrative register data for the complete population of Sweden and examine changes in intergenerational proximity between 1980 and 2010, using couples at the birth of their first child as the study population. An explicit policy goal of tertiary expansion was to widen the geographical access to tertiary education and the enrolment grew at newer regional institutions during this period. We additionally explore if this policy of regional expansion influenced average distance to parents. We find that intergenerational distances increased over the study period and that this was mainly attributed to the increased enrolment at traditional, older, universities. Copyright © 2015 John Wiley & Sons, Ltd.
Experimental Research Methods in Migration: From Natural to True Experiments
Authors: Baláž Vladimír , Williams Allan M 
Published: August 2015

AbstractMigration researchers have demonstrated relatively limited engagement with experimental research. The strongest engagement has been with natural experiments, which observe actual migrant behaviour, typically analysing migration behaviour before and after particular events, but have limitations in terms of control over the ‘experiment’. In contrast, researchers have relatively neglected the contribution of true experiments involving the manipulation or simulation of changes in the environment or institutions that shape migration. The paper compares the relative strengths of two types of true experiments – field and laboratory – in terms of their validity and reliability, reviews their current application in migration studies, and sets out opportunities to develop future research around these methodologies. Copyright © 2015 John Wiley & Sons, Ltd.
Have Destination Choices of Foreign Residents Contributed to Reducing Regional Population Disparity in Japan? Analysis Based on the 2010 Population Census Microdata
Authors: Hanaoka Kazumasa , Ishikawa Yoshitaka , Takeshita Shuko 
Published: August 2015

AbstractIn relation to the beginning of Japan's total population decline, the problem of regional disparity has been attracting a great deal of attention in the country. Have the destination choices of foreign residents in recent years contributed to reducing such disparity? The purpose of this study is to analyse the destination choices of new immigrants and foreign residents moving within Japan in the period 2005–2010, using microdata from the 2010 Population Census. The results are compared with those obtained from the period 1995–2000. Three major findings are obtained: First, the empirical validities of three theoretical perspectives (effect of labour market conditions, attraction to co‐ethnic communities, and spatial distribution of marital opportunities) are confirmed to a similar extent in this study as in the previous period. Second, the pull effect of the service industry is much larger than that of the manufacturing industry, for both new immigration and internal migration. Finally, although there is an obvious distance–decay tendency in internal migration, foreign residents (particularly Chinese residents) have shown the tendency of dispersal, including suburbanization. However, if the destination choices of foreign residents observed in 2005–2010 as a whole continue into the future, they would eventually worsen rather than alleviate the disparity. Copyright © 2015 John Wiley & Sons, Ltd.
The importance of edges in reactive ion etched graphene nanodevices
Authors: Bischoff Dominik , Simonet Pauline , Varlet Anastasia , Overweg Hiske C. , Eich Marius , Ihn Thomas , Ensslin Klaus 
Published: August 2015

magnified imagePatterned graphene nanodevices are promising candidates for nano‐ and quantum‐electronics. Low temperature electronic transport in reactive ion etched graphene nanodevices is typically governed by charge localization manifesting itself in the appearance of Coulomb blockade. The disorder originating from non‐perfect graphene edges was identified as being the dominant reason for the stochastic charge localization in graphene nanoribbons. It was found that electrons can localize along the edges on length scales much longer than the physical disorder length. Such states localized along the edge can even leak out of the nanoribbon into adjacent wide graphene leads suggesting that a possibly existing confinement gap is not required to explain transport properties of etched graphene nanodevices. These insights are then used to improve the understanding of transport in graphene quantum dots where Coulomb blockade is typically more regular than in nanoribbons. It is shown that non‐overlapping Coulomb diamonds can be observed even in a regime where three states of localized charge need to be passed in series by an electron traveling from source to drain contact. This counter‐intuitive observation is explained by higher order co‐tunneling through the localized states in the nanoribbons connecting the graphene dot to the leads.
magnified image(© 2015 WILEY‐VCH Verlag GmbH &Co. KGaA, Weinheim)
Generation of (M = K, Rb, Cs, 2n = 80–220) by laser ablation of graphene
Authors: Bao Xiaodi , Kong Xianglei 
Published: August 2015

RationaleThe yield of endohedral metallofullerene (EMF) ions is greatly related to the encaged metal atoms. For alkali metals, the generation of corresponding large‐sized monometallofullerene ions by traditional methods is still difficult. The aim of this work is to study the generation and the distribution of alkali‐metallofullerene ions by the method of laser ablation with graphene as the precursor.MethodsThe experiment was performed with a Fourier transform ion cyclotron (FTICR) mass spectrometer. Mass spectra were obtained by laser ablation of the mixtures of graphene and KCl, RbCl or CsCl in the positive ion mode. Collision‐induced dissociation (CID) experiments were also performed for some selected ions.ResultsEMF ions of
(M = K, Rb, Cs, 2n = 80–220) can be generated by using graphene as the precursor. Other EMF ions with smaller sizes, including
, were also observed under the optimized experimental conditions. CID experiments of some selected ions confirmed their endohedral structures.ConclusionsMetallofullerene ions of
(M = K, Rb, Cs, 2n = 80–220) were generated by laser ablation of graphene and corresponding metal salts. Compared with previous results of alkaline earth metals, the yields of EMF ions are generally lower. However, for large‐sized EMF ions, the relative intensities of EMF ions to their corresponding fullerene ions
/
generally increase with the increase in cluster sizes, which is opposite to the trend observed for alkaline earth metals. Copyright © 2015 John Wiley & Sons, Ltd.
The in situ gas‐phase formation of a C‐glycoside ion obtained during electrospray ionization tandem mass spectrometry. A unique intramolecular mechanism involving an ion‐molecule reaction
Authors: Banoub Joseph H. , Demian Wael L. L. , Piazzetta Paolo , Sarkis George , Kanawati Basem , Lafont Dominique , Laurent Nicolas , Vaillant Celine , Randell Edward , Giorgi Gianluca , Fridgen Travis D. 
Published: August 2015

RationaleThis study examines the electrospray ionization mass spectrometry (ESI‐MS), in‐source collision‐induced dissociation (CID) fragmentation and low‐energy collision‐induced dissociation tandem mass spectrometry (CID‐MS/MS) of a synthetic pair of β‐ and α‐anomers of the amphiphilic cholesteryl polyethoxy neoglycolipids containing the 2‐azido‐2‐deoxy‐D‐galactosyl‐D‐GalN3 moiety. We describe the novel and unique in situ gas‐phase formation of a C‐glycoside ion formed during all these gas‐phase processes and propose a reasonable mechanism for its formation.MethodsThe synthetic amphiphilic glycolipids were composed of the 2‐deoxy‐2‐azido‐D‐galactosyl moiety (GalN3, the hydrophilic part) covalently attached to a polyethoxy spacer which is covalently linked to the cholesteryl moiety (hydrophobic part). The 2‐azido‐2‐deoxy‐α‐ and β‐D‐galactosyl‐containing glycolipids were studied by in‐time and in‐space ESI‐MS and CID‐MS/MS in positive ion mode, with quadrupole ion trap (QIT), quadrupole‐quadrupole‐time‐of‐flight (QqTOF), and Fourier transform ion cyclotron resonance (FTICR) instruments.ResultsConventional single‐stage ESI‐MS analysis showed the formation of the protonated molecule. During the single‐stage ESI‐MS analysis and the CID‐MS/MS of the [M+H]+ and [M+NH4]+ adducts obtained from both glycolipid anomers, the presence of a series of specific product ions with different intensities was observed, consistent with the [C‐glycoside+H–N2]+, [cholestadiene+H]+, 2‐deoxy‐2‐D‐azido‐galactosyl [GalN3]+, [GalNH]+ and [sugar−Spacer+H]+ ions.ConclusionsThe gas‐phase formation of the [C‐glycoside+H–N2]+ ion isolated from the glycolipid anomers was observed during both the ESI‐MS of the glycolipids and the CID‐MS/MS analyses of the [M+H]+ ions and it was found to occur by an intramolecular rearrangement involving an ion‐molecule complex. CID‐QqTOF‐MS/MS and CID‐FTICR‐MS2 analysis allowed the differentiation of the two glycolipid anomers and showed noticeable variation in the intensities of the product ions. Copyright © 2015 John Wiley & Sons, Ltd.
MZDASoft: a software architecture that enables large‐scale comparison of protein expression levels over multiple samples based on liquid chromatography/tandem mass spectrometry
Authors: Ghanat Bari Mehrab , Ramirez Nelson , Wang Zhiwei , Zhang Jianqiu (Michelle) 
Published: August 2015

RationaleWithout accurate peak linking/alignment, only the expression levels of a small percentage of proteins can be compared across multiple samples in Liquid Chromatography/Mass Spectrometry/Tandem Mass Spectrometry (LC/MS/MS) due to the selective nature of tandem MS peptide identification. This greatly hampers biomedical research that aims at finding biomarkers for disease diagnosis, treatment, and the understanding of disease mechanisms. A recent algorithm, PeakLink, has allowed the accurate linking of LC/MS peaks without tandem MS identifications to their corresponding ones with identifications across multiple samples collected from different instruments, tissues and labs, which greatly enhanced the ability of comparing proteins. However, PeakLink cannot be implemented practically for large numbers of samples based on existing software architectures, because it requires access to peak elution profiles from multiple LC/MS/MS samples simultaneously.MethodsWe propose a new architecture based on parallel processing, which extracts LC/MS peak features, and saves them in database files to enable the implementation of PeakLink for multiple samples. The software has been deployed in High‐Performance Computing (HPC) environments. The core part of the software, MZDASoft Parallel Peak Extractor (PPE), can be downloaded with a user and developer's guide, and it can be run on HPC centers directly. The quantification applications, MZDASoft TandemQuant and MZDASoft PeakLink, are written in Matlab, which are compiled with a Matlab runtime compiler. A sample script that incorporates all necessary processing steps of MZDASoft for LC/MS/MS quantification in a parallel processing environment is available. The project webpage is http://compgenomics.utsa.edu/zgroup/MZDASoft.ResultsThe proposed architecture enables the implementation of PeakLink for multiple samples. Significantly more (100%–500%) proteins can be compared over multiple samples with better quantification accuracy in test cases.ConclusionMZDASoft enables large‐scale comparison of protein expression levels over multiple samples with much larger protein comparison coverage and better quantification accuracy. It is an efficient implementation based on parallel processing which can be used to process large amounts of data. Copyright © 2015 John Wiley & Sons, Ltd.
Gas‐phase fragmentation of the N‐oxide and N‐hydroxylated derivatives of retrorsine using liquid chromatography/electrospray ionization quadrupole time‐of‐flight tandem mass spectrometry
Authors: Jahouh Farid , Marongiu Fabio , Serra Maria Paola , Laconi Ezio , Banoub Joseph 
Published: August 2015

RationaleWe report the electrospray ionization mass spectrometry and low‐energy collision‐induced dissociation tandem mass spectrometry (CID‐MS/MS) analysis of a pyrrolizidine alkaloid extract containing both retrorsine [C18H25NO6] and its N‐oxide [C18H25NO7] and N‐hydroxyl [C18H26NO7] derivatives measured with a QqTOFMS hybrid instrument.MethodsA solution of the pyrrolizidine alkaloid extract containing retrorsine and its N‐oxide and N‐hydroxyl derivatives was directly infused into an electrospray ionization‐quadrupole‐time‐of‐flight (ESI‐QTOF) mass spectrometer and product ion scans of the protonated molecules of each species were acquired. Labile protons of each compound were deuterated and computational energy calculations of the proposed structures of the product ions were used to determine the fragmentation pathways of retrorsine and its N‐oxide and N‐hydroxyl derivatives.ResultsESI‐MS of the pyrrolizidine alkaloid extract containing retrorsine and its N‐oxide and N‐hydroxyl derivatives afforded the protonated retrorsine [M1 + H]+ at m/z 352.1760 and the protonated retrorsine N‐oxide [M2 + H]+ at m/z 368.1631 in addition to the formation of the unexpected protonated N‐hydroxyl radical [M3 + H]+• at m/z 369.1686. CID‐MS/MS of this series of protonated molecules allowed the evaluation of their gas‐phase fragmentations and the establishment of their fragmentation pathways. It was also found that several product ions could be assigned to different structures. Deuterium exchange and computational energy calculations allowed us to determine the most probable structures for the characterized product ions.ConclusionsTo our knowledge, the identification of the protonated retrorsine N‐hydroxyl radical [M3 + H]+• is reported for the first time. In addition, the MS/MS results can be used for the identification of retrorsine and its N‐oxide and N‐hydroxyl derivatives in different complex biological matrices. Copyright © 2015 John Wiley & Sons, Ltd.