bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel approach to the analysis of SUMOylation with the independent use of trypsin and elastase digestion followed by database searching utilising consecutive residue addition to lysine
Authors: Chicooree Navin , Griffiths John R. , Connolly Yvonne , Tan Chong‐Teik , Malliri Angeliki , Eyers Claire E. , Smith Duncan L. 
Published: December 2012

RATIONALEIdentification of sites of protein SUMOylation is of great importance due its functional diversity within the cell. To date, most approaches to this problem rely on site‐directed mutagenesis and/or highly specialised mass spectrometry approaches. We present a novel alternative approach to the site mapping of SUMOylation using trypsin and elastase digestion, routine mass spectrometry and an unbiased isotag database searching strategy.METHODSSUMOylated protein samples were digested with a number of enzymes and the resulting peptides separated using liquid chromatography. Analysis was carried out on both linear ion trap Orbitrap and quadrupole‐time‐of‐flight (Q‐TOF)‐based mass spectrometers equipped with electrospray ionisation. The data files were subsequently searched using the Mascot algorithm with multiple variable tag modifications corresponding to SUMO‐derived fragments. The utility of this approach was demonstrated with di‐SUMO 2, di‐SUMO 3, SUMO 1‐RanGap418‐587 1 and an enriched population of SUMOylated proteins.RESULTSUnbiased database searches led to the identification of a number of analytically useful isotags ranging in length from two to four residues. Isopeptide fragments were generated including QTGG (di‐SUMO‐2/3), TGG (di‐SUMO‐2/3) and GG (SUMO‐1). The method was validated by successfully mapping a number of sites of SUMO modification on SUMO‐modified proteins enriched from a cell lysate.CONCLUSIONSThis combination of relaxed enzyme specificity, shortened isotag generation and unbiased database searching enabled confident identification of novel analytically useful SUMOylated isopeptides without a requirement for mutagenesis. Copyright © 2012 John Wiley & Sons, Ltd.
Negative ion fragmentations of disulfide‐containing cross‐linking reagents are competitive with aspartic acid side‐chain‐induced cleavages
Authors: Calabrese Antonio N. , Wang Tianfang , Bowie John H. , Pukala Tara L. 
Published: December 2012

RATIONALEIt has been shown that the disulfide moiety in the chemical cross‐linking reagent dithiobis(succinimidyl)propionate (DSP), which is similar in structure to the natural cystine disulfide, cleaves preferentially to the peptide backbone in the negative ion mode. However, the tandem mass (MS/MS) spectra of peptides in the negative ion mode are often dominated by products arising from low‐energy, side‐chain‐induced processes, which may compete with any facile cross‐linker fragmentations and complicate identification of chemical cross‐links in a complex mixture.METHODSTwo disulfide‐containing crosslinking reagents similar to DSP, but with varying spacer arm lengths, were synthesized and the MS/MS spectra of several model peptides cross‐linked with these reagents were investigated. Theoretical calculations were used to describe the energetics of the cross‐linker fragmentations as well as several low‐energy side‐chain‐induced fragmentations which compete with disulfide cleavages.RESULTSAltering the spacer arm length of the cross‐linker, such that there is one methylene group less than in DSP, results in a more facile cleavage process, whilst the opposite is true when a methylene group is added. Of the low‐energy side‐chain‐induced fragmentations studied, only those from aspartic acid compete significantly with those of the cross‐linker disulfide.CONCLUSIONSLow‐energy cleavage processes from aspartic acid that compete with cross‐linker fragmentations occur in the negative ion MS/MS spectra of the cross‐linked peptides, irrespective of the spacer arm length. Other fragmentation pathways do not significantly interfere with low‐energy disulfide cleavage, making the presence of additional product ions in the MS/MS spectrum diagnostic for the presence of aspartic acid. Copyright © 2012 John Wiley & Sons, Ltd.
Study on the intermediate ions formed by glutathione peroxidase mimic 2,2'‐ditellurobis(2‐deoxy‐β‐cyclodextrin) by electrospray ionization mass spectrometry
Authors: Jiao Aiquan , Yang Na , Xu Xueming , Jin Zhengyu 
Published: December 2012

RATIONALE2,2'‐Ditellurobis(2‐deoxy‐β‐cyclodextrin) (2‐TeCD) is one of the most well‐known glutathione peroxidase (GPx) mimics. However, because the critical reaction intermediates had not previously been isolated or directly detected due to its short lifetime, the catalytic mechanism of 2‐TeCD is not very clear and further experiments are needed to characterize each of the intermediates in the catalytic cycle.METHODSUsing electrospray ionization mass (and tandem) spectrometry (ESI‐MS and ESI‐MS/MS) experiments, the decomposition of hydrogen peroxide at the expense of glutathione (GSH) catalyzed by 2‐TeCD was monitored on‐line.RESULTSThe key intermediates were successfully intercepted and structurally characterized for the first time by coupling a microreactor on‐line to the ESI ion source, which permitted the fast screening of intermediates directly from solution.CONCLUSIONSThe catalytic mechanism of 2‐TeCD catalysis has been elaborated based on mass spectrometric data and exerted its peroxidase activity via tellurol, tellurenic acid, and tellurosulfide, in analogy with natural GPX. Copyright © 2012 John Wiley & Sons, Ltd.
Agile coaching for global software development
Authors: Paasivaara Maria , Lassenius Casper 
Published: December 2012

SUMMARYThis paper presents a case study on building a successful agile coaching team focusing on global software development projects in an international Nordic‐based software company. We describe how the team of eight coaches was built, and how the coaches work together as a team using agile practices, such as weekly iterations, backlogs, and daily stand‐ups. Furthermore, we describe their ‘deep and narrow’ approach to working closely with case projects, and the benefits to the coached projects. We describe the main challenges in building the coaching activities in a globally distributed company. The paper concludes with a set of lessons learned for coaching globally distributed projects and a discussion of the future plans for scaling up coaching by building a global coaching network within the company. We collected the data using 13 semi‐structured interviews of the coaching team members, and personnel from four coached case projects. Copyright © 2012 John Wiley & Sons, Ltd.
Inter‐Cloud architectures and application brokering: taxonomy and survey
Authors: Grozev Nikolay , Buyya Rajkumar 
Published: December 2012

SUMMARYAlthough Cloud computing itself has many open problems, researchers in the field have already made the leap to envision Inter‐Cloud computing. Their goal is to achieve better overall Quality of Service (QoS), reliability and cost efficiency by utilizing multiple clouds. Inter‐Cloud research is still in its infancy, and the body of knowledge in the area has not been well defined yet. In this work, we propose and motivate taxonomies for Inter‐Cloud architectures and application brokering mechanisms. We present a detailed survey of the state of the art in terms of both academic and industry developments (20 projects), and we fit each project onto the discussed taxonomies. We discuss how the current Inter‐Cloud environments facilitate brokering of distributed applications across clouds considering their nonfunctional requirements. Finally, we analyse the existing works and identify open challenges and trends in the area of Inter‐Cloud application brokering. Copyright © 2012 John Wiley & Sons, Ltd.
Systematic review of sonographic findings of placental mesenchymal dysplasia and subsequent pregnancy outcome
Authors: Nayeri U. A. , West A. B. , Grossetta Nardini H. K. , Copel J. A. , Sfakianaki A. K. 
Published: December 2012

ABSTRACTObjectiveTo describe the sonographic features and pregnancy outcomes of placental mesenchymal dysplasia (PMD), an entity often misdiagnosed as molar pregnancy.MethodsWe reviewed PMD cases from our institution and performed a systematic review of the existing literature. Inclusion criteria for the review were diagnosis of PMD as defined by placental pathology, description of placental morphology on antenatal ultrasound and reporting of pregnancy outcomes.ResultsWe found three cases of PMD at our institution. Patient 1 had elevated human chorionic gonadotropin (hCG) and an enlarged, hydropic placenta at 13 weeks, suggestive of a molar pregnancy. Patient 2 also had elevated hCG with large, vascular placental lakes on ultrasound suggesting placenta accreta or molar pregnancy. Case 3 involved placentomegaly and fetal anomalies suggestive of Beckwith–Wiedemann syndrome. From the literature review, 61 cases met the inclusion criteria. The most common sonographic features included enlarged (50%) and cystic (80%) placenta with dilated chorionic vessels. Biochemical aneuploidy screening abnormalities were relatively common as were fetal anomalies, Beckwith–Wiedemann syndrome and other genetic abnormalities. Pregnancy complications included intrauterine growth restriction (IUGR; 33%), intrauterine fetal death (IUFD; 13%), and preterm labor (33%). Pregnancies without fetal anomalies, IUGR, IUFD or preterm labor had normal neonatal outcomes despite PMD (9%).ConclusionsThe differential diagnosis of PMD includes molar pregnancy and other placental vascular anomalies. PMD is associated with adverse pregnancy outcome, so heightened surveillance with genetic evaluation, serial growth scans and third‐trimester assessment of wellbeing should be considered. PMD must be differentiated from gestational trophoblastic disease because management and outcomes differ. Copyright © 2012 ISUOG. Published by John Wiley & Sons, Ltd.
The Utility of Effective Theories
Authors: Wells James D. 
Published: December 2012

Abstract“Effective Theories” are theories because they are able to organize phenomena under an efficient set of principles, and they are effective because it is not impossibly complex to compute outcomes. The only way a theory can be effective is if it is manifestly incomplete. “Everything affects anything” is generally correct, but it saps confidence in our ability to predict outcomes. Effective Theories modify this depressing maxim by pointing out that “most things are irrelevant for all practical purposes.” A tree falling in Peru does not appreciably affect a canon ball’s flight in Australia. Any good Effective Theory systematizes what is irrelevant for the purposes at hand. In short, an Effective Theory enables a useful prediction with a finite number of input parameters.
Effective Theories and Elementary Particle Masses
Authors: Wells James D. 
Published: December 2012

AbstractThe concepts of effective theory have a rich history in particle physics. The early days of effective theories have many examples, including Fermi’s theory of nucleon decay and chiral lagrangian dynamics for pion scattering. These examples are touched upon briefly before going to the most pressing issue of today, which is the origin of elementary particle masses. The problem of mass generation is first described, where it is shown that simply writing down mass terms manifestly breaks cherished symmetries. It is then shown that spontaneous symmetry breaking cures this problem. The influence of effective field theory is then addressed, where it is shown that the smallness of neutrino masses nicely conforms with our intuition, but the weak-scale value of the Higgs boson mass is confusing. The chapter concludes with an essay describing this mystery and what the resolutions might be.
High CD44s expression is associated with the EMT expression profile and intrahepatic dissemination of hepatocellular carcinoma after local ablation therapy
Authors: Mima Kosuke , Hayashi Hiromitsu , Imai Katsunori , Kuroki Hideyuki , Nakagawa Shigeki , Okabe Hirohisa , Chikamoto Akira , Watanabe Masayuki , Beppu Toru , Baba Hideo 
Published: December 2012

AbstractBackground/purposeLocal ablation therapy (LAT) is a widely used treatment for hepatocellular carcinoma (HCC) because it is less invasive than hepatic resection. The precise molecular mechanism underlying local HCC recurrence after LAT is largely unknown. The CD44 standard isoform (CD44s) is involved in epithelial—mesenchymal transition (EMT) in HCC. We investigate the significance of CD44s expression and EMT expression profile in local HCC recurrence after LAT.MethodsWe studied the expression levels of CD44s, EMT expression profile (E‐cadherinlow/vimentinhigh expression) and their association with clinicopathological factors in 30 HCC samples from patients with locally recurrent HCCs after LAT following hepatic resection. The alterations of CD44s expression was compared with those in initial HCCs from 150 patients without prior any anticancer treatment including LAT.ResultsA high CD44s expression was significantly associated with the EMT expression profile (P = 0.002), and it was also detected with a higher frequency in the locally recurrent HCCs after LAT compared to initial HCCs (P < 0.001). In addition, high CD44s expression was associated with the intrahepatic dissemination of HCC after LAT (P = 0.006).ConclusionsThese results suggest that high CD44s expression is associated with the aggressive recurrence pattern via EMT after LAT for HCC.
An opportunistic pathogen isolated from the gut of an obese human causes obesity in germfree mice
Authors: Fei Na , Zhao Liping 
Published: December 2012

Abstract
Lipopolysaccharide endotoxin is the only known bacterial product which, when subcutaneously infused into mice in its purified form, can induce obesity and insulin resistance via an inflammation-mediated pathway. Here we show that one endotoxin-producing bacterium isolated from a morbidly obese human’s gut induced obesity and insulin resistance in germfree mice. The endotoxin-producing Enterobacter decreased in relative abundance from 35% of the volunteer’s gut bacteria to non-detectable, during which time the volunteer lost 51.4 kg of 174.8 kg initial weight and recovered from hyperglycemia and hypertension after 23 weeks on a diet of whole grains, traditional Chinese medicinal foods and prebiotics. A decreased abundance of endotoxin biosynthetic genes in the gut of the volunteer was correlated with a decreased circulating endotoxin load and alleviated inflammation. Mono-association of germfree C57BL/6J mice with strain Enterobacter cloacae B29 isolated from the volunteer’s gut induced fully developed obesity and insulin resistance on a high-fat diet but not on normal chow diet, whereas the germfree control mice on a high-fat diet did not exhibit the same disease phenotypes. The Enterobacter-induced obese mice showed increased serum endotoxin load and aggravated inflammatory conditions. The obesity-inducing capacity of this human-derived endotoxin producer in gnotobiotic mice suggests that it may causatively contribute to the development of obesity in its human host.
Evidence of long‐term structured cuckoo parasitism on individual magpie hosts
Authors: Molina‐Morales Mercedes , Gabriel Martínez Juan , Martín‐Gálvez David , A. Dawson Deborah , Rodríguez‐Ruiz Juan , Burke Terry , Avilés Jesús M. 
Published: December 2012

SummaryBrood parasites usually reduce their host's breeding success, resulting in strong selection for the evolution of host defences. Intriguingly, some host individuals/populations show no defence against parasitism, which has been explained within the frame of three different evolutionary hypotheses. One of these hypotheses posits that intermediate levels of defence at the population level may result from nonrandom distribution of parasitism among host individuals (i.e. structured parasitism). Empirical evidence for structured brood parasitism is, however, lacking for hosts of European cuckoos due to the absence of long‐term studies.Here, we seek to identify the patterns of structured parasitism by studying great spotted cuckoo parasitism on individual magpie hosts over five breeding seasons. We also aim to identify whether individual characteristics of female magpies and/or their territories were related to the status of repeated parasitism.We found that 28·3% of the females in our population consistently escaped from cuckoo parasitism. Only 11·3% of females were always parasitized, and the remaining 60·4% changed their parasitism status. The percentage of females that maintained their status of parasitism (i.e. either parasitized or nonparasitized) between consecutive years varied over the study. Females that never suffered cuckoo parasitism built bigger nests than parasitized females at the beginning of the breeding season and smaller nests than those of parasitized females later in the season. Nonparasitized females also moved little from year to year and preferred areas with different characteristics over the course of the breeding season than parasitized females. Overall, females escaping from cuckoo parasitism reared twice as many chicks per year than those that were parasitized.In conclusion, our study reveals for first time the existence of a structured pattern of cuckoo parasitism based on phenotypic characteristics of individual hosts and of their territories.
The evolutionary ecology of dwarfism in three‐spined sticklebacks
Authors: MacColl Andrew D. C. , Nagar Aliya El , de Roij Job 
Published: December 2012

SummaryBody size is a defining phenotypic trait, but the ecological causes of its evolution are poorly understood. Most studies have considered only a single putative causal agent and have failed to recognise that different environmental agents are often correlated.Darwin suggested that although trait variation across populations is often associated with abiotic variation, evolution is more likely to be driven by biotic factors correlated with the abiotic variation. This hypothesis has received little explicit attention.We use structural equation modelling to quantify the relative importance of abiotic (pH, metal concentrations) and biotic (competition, predation) factors in the evolution of body size in three‐spined sticklebacksGasterosteus aculeatuson the island of North Uist, Scotland. We combine phenotypic data from multiple isolated populations, detailed characterisation of their environment and a common garden experiment that establishes the genetic basis of size differences.Three‐spined sticklebacks on North Uist show almost unprecedented intraspecific evolution of body size that has taken place rapidly (<16 000 years). The smallest fish mature at only 7% of the mass of ancestral, anadromous fish. Dwarfism is associated with reduced abundance of a smaller competitor species, the nine‐spined sticklebackPungitius pungitius, and with low pH indicative of poor resource conditions. Dwarfism also tends to occur where an important predator, the brown troutSalmo trutta, is also small. The abundance ofP. pungitiusand the size ofS. truttaare themselves related to underlying abiotic environmental variation.Despite the close association between abiotic and biotic factors across populations, our results support Darwin's hypothesis that biotic factors, associated with variation in the abiotic environment, are more important in explaining evolution than is abiotic variationper se. This study demonstrates the importance of considering the relationships between environmental variables before conclusions can be drawn about the causes of (body size) evolution on islands.
Suitability of three Ostrinia species as hosts for Macrocentrus cingulum: A comparison of their encapsulation abilities
Authors: Havard Sébastien , Pélissier Céline , Ponsard Sergine , Campan Erick D. M. 
Published: December 2012

AbstractTwo cornborer species, Ostrinia furnacalis (Lepidoptera: Crambidae) and O. nubilalis, are major corn pests in Asia and Europe, respectively. In both continents, the larval endoparasitoid Macrocentrus cingulum (Hymenoptera: Braconidae) develops on another, closely related stemborer, O. scapulalis, which feeds on mugwort and other dicotyledons. M. cingulum also emerges from O. furnacalis in Asia and O. nubilalis in North America, but not from O. nubilalis in Europe. We assessed the ability of three populations of each of the three Ostrinia species to encapsulate foreign bodies of a size similar to that of a M. cingulum egg. We conclude that variations in encapsulation ability alone cannot account for the differences observed in the field between parasite emergence rates in these different host species and geographic areas.
The CAP post 2013: Ineffective for Mitigating Climate Change
Authors: Freibauer Annette , Osterburg Bernhard , Reiter Karin , Röder Norbert 
Published: December 2012

summaryThe CAP post 2013: Ineffective for Mitigating Climate ChangeAgriculture emits more than 11 per cent of the greenhouse gases (GHG) from the EU‐27. In this article we point out the shortcomings of the European Commission′s Reform Proposals for the Common Agricultural Policy (CAP) towards effective climate change mitigation and present some specifications to be included in the main text or the implementing regulations to support European agriculture in its transition towards climate‐friendly production. The Proposals set the aspiration to respond to climate change but fail to provide incentives to make a quantifiable step. Yet the CAP Reform Proposals can still set enabling framework conditions for mitigation, define binding targets and produce verifiable mitigation results. This article proposes inter alia: (1) to evaluate the GHG impacts of CAP measures and stop negative incentives e.g. support of intensive land use on carbon‐rich soils; (2) fostering a learning process by making GHG mitigation measures with verifiable results a mandatory part of the 2nd Pillar; (3) implementing measures along the food processing chain via improved resource efficiency, investments, innovation and knowledge transfer, and not just through area‐based measures; and (4) providing a separate CAP budget for mitigating CO2 emissions from agricultural soils, which are outside the EU Climate and Energy Package.
Assessing Systems‐based Practice
Authors: Chen Esther H. , O'Sullivan Patricia S. , Pfennig Camiron L. , Leone Katrina , Kessler Chad S. 
Published: December 2012

AbstractThe conceptual definition of systems‐based practice (SBP) does not easily translate into directly observable actions or behaviors that can be easily assessed. At the Academic Emergency Medicine consensus conference on education research in emergency medicine (EM), a breakout group presented a review of the literature on existing assessment tools for SBP, discussed the recommendations for research tool development during breakout sessions, and developed a research agenda based on this discussion.