bluuebunny/crossref_metadata_2025_split huggingface dataset:
The long intervention: continuity in the Balkan theatre
Authors: WOODWARD SUSAN L. 
Published: September 2013

AbstractGreat Power intervention in the Balkans since the late nineteenth century shows a striking continuity in motivations, methods, and consequences. The article proposes that current intervention practices are largely a response to the Balkan theatre in the 1990s and thus institutionalise this continuity more than arguments about normative and institutional change since 1990 suggest. Three continuities are emphasised: the concept of a ‘turbulent frontier’ to explain an unintended dynamic of nearly continuous intervention, the importance of local actors' interests (the pull of intervention) alongside those of major power interests (the push), and the primary influence on domestic orders and cause of the ‘turbulence’ of economic relations.
Characterization of a novel international clonal complex (CC32) ofAcinetobacter baumanniiwith epidemic potential
Authors: DA SILVA G. J. , VAN DER REIJDEN T. , DOMINGUES S. , MENDONÇA N. , PETERSEN K. , DIJKSHOORN L. 
Published: September 2013

SUMMARYTwelve non-replicateAcinetobacter baumanniiisolates from five European hospitals, Kuwait, and the US military healthcare system collected between 1980 and 2005 revealed a new clone, CC32. These included representative isolates of outbreaks/cross-infections. Antimicrobial susceptibility and carbapenem-resistant genetic traits varied. The widespread occurrence, the association with an outbreak and the carbapenem resistance indicate that CC32 has epidemic potential.
Predictors of influenza in the adult population during seasonal and A(H1N1)pdm09 pandemic influenza periods
Authors: GEFENAITE G. , TACKEN M. , KOLTHOF J. , MULDER B. , KOREVAAR J. C. , STIRBU-WAGNER I. , BOS J. , STOLK R. P. , HAK E. 
Published: September 2013

SUMMARYWe aimed to assess whether the characteristics of influenza-like illness (ILI) cases in the general population were similar during the seasonal and pandemic A(H1N1)pdm09 influenza periods. We conducted a study using a general population database, which included demographic (sex, age) and clinical (underlying medical conditions, influenza vaccination status) information on more than 80 000 subjects. We assessed the most important predictors of ILI during each season by using multiple logistic regression. We descriptively compared whether they were similar during different seasons. The model, including all demographic and clinical characteristics, showed that age ⩾60 years decreased the odds for ILI by 52% and 81% during the seasonal and A(H1N1)pdm09 pandemic periods, respectively. Being vaccinated decreased the odds of ILI for seasonal influenza by 32%, while suffering from the comorbidities other than lung or cardiovascular diseases doubled the odds of ILI during the A(H1N1)pdm09 pandemic.
SUPERNILPOTENCE PREVENTS DUALIZABILITY
Authors: BENTZ WOLFRAM , MAYR PETER 
Published: September 2013

AbstractWe address the question of the dualizability of nilpotent Mal’cev algebras, showing that nilpotent finite Mal’cev algebras with a nonabelian supernilpotent congruence are inherently nondualizable. In particular, finite nilpotent nonabelian Mal’cev algebras of finite type are nondualizable if they are direct products of algebras of prime power order. We show that these results cannot be generalized to nilpotent algebras by giving an example of a group expansion of infinite type that is nilpotent and nonabelian, but dualizable. To our knowledge this is the first construction of a nonabelian nilpotent dualizable algebra. It has the curious property that all its nonabelian finitary reducts with group operation are nondualizable. We were able to prove dualizability by utilizing a new clone theoretic approach developed by Davey, Pitkethly, and Willard. Our results suggest that supernilpotence plays an important role in characterizing dualizability among Mal’cev algebras.
Symmetry breaking gives rise to energy spectra of three states of matter
Authors: Bolmatov Dima , Musaev Edvard T. , Trachenko K. 
Published: September 2013

AbstractA fundamental task of statistical physics is to start with a microscopic Hamiltonian, predict the system's statistical properties and compare them with observable data. A notable current fundamental challenge is to tell whether and how an interacting Hamiltonian predicts different energy spectra, including solid, liquid and gas phases. Here, we propose a new idea that enables a unified description of all three states of matter. We introduce a generic form of an interacting phonon Hamiltonian with ground state configurations minimising the potential. Symmetry breakingSO(3) toSO(2), from the group of rotations in reciprocal space to its subgroup, leads to emergence of energy gaps of shear excitations as a consequence of the Goldstone theorem and readily results in the emergence of energy spectra of solid, liquid and gas phases.
A TFG–TEC nuclear localization mutant forms complexes with the wild-type TFG–TEC oncoprotein and suppresses its activity
Authors: Lim Bobae , Kim Ah-young , Jun Hee Jung , Kim Jungho 
Published: September 2013

Human EMCs (extraskeletal myxoid chondrosarcomas) are soft tissue tumours characterized by specific chromosomal abnormalities. Recently, a proportion of EMCs were found to harbour a characteristic translocation, t(3;9)(q11-12;q22), involving the TFG (TRK-fused gene) at 3q11-12 and the TEC (translocated in extraskeletal chondrosarcoma) gene at 9q22. The present study used both in vitro and in vivo systems to show that the TFG–TEC protein self-associates, and that this is dependent upon the CC (coiled-coil) domain (amino acids 97–124), the AF1 (activation function 1) domain (amino acids 275–562) and the DBD (DNA-binding domain) (amino acids 563–655). The TFG–TEC protein also associated with a mutant NLS-TFG–TEC (AAAA) protein, which harbours mutations in the NLS (nuclear localization signal). Subcellular localization assays showed that the NLS mutant TFG–TEC (AAAA) protein interfered with the nuclear localization of wild-type TFG–TEC. Most importantly, the mutant protein inhibited TFG–TEC-mediated transcriptional activation in vivo. Thus mutations in the TFG–TEC NLS yield a dominant-negative protein. These results show that the biological functions of the TFG-TEC oncogene can be modulated by a dominant-negative mutant.
Youth, family change and welfare arrangements
Authors: Moreno Luis , Marí-Klose Pau 
Published: September 2013

ABSTRACT
This paper analyzes the main characteristics and welfare rationale of the Mediterranean typology. Familism, female employment and care are singled out as three representative areas which provide data on the dynamics of continuity and change in the Southern European countries under examination. Particular attention is paid to the increasing female participation in the labour market and the gradual disappearance of the so-called Mediterranean ‘superwomen’. The process of female labour activation is already having a great impact in all activities concerned with the type of care traditionally carried out within Mediterranean households. Final remarks stress the need to pay attention in future research to ongoing societal changes which are bound to have knock-on consequences for Southern European welfare as we have known it until now.
The Southern European migrant-based care model
Authors: Da Roit Barbara , González Ferrer Amparo , Moreno-Fuentes Francisco Javier 
Published: September 2013

ABSTRACT
The development of personal social services and female employment is intertwined, not only in the domain of childcare. With the ageing of the population, the changing forms of care and the developments in the eldercare labour market become crucial issues. The new risk of dependency represents a challenge, but also an opportunity. This paper provides an overview of the relationship between the development of long-term care policies and services in distinct European countries and female employment in the care sector. Whereas Northern European countries have developed policies in the field at an earlier stage and continental countries intervened with new policies in the last 10–15 years, in Southern Europe policies remain weak and fragmented. The paper concentrates on the case of Southern European countries, where the weakness of social policies and low development of services did not prevent the rise of a new care labour market. Next to still low employment rates among women, long-term care tends to be provided mainly by migrant care workers often in the underground economy regardless of their legal status. The last development is a key issue for Southern European countries, as discussed in the paper, not only for the current consequences on migrant workers, older people and their families, but also because it is likely to structure any possible future development in long-term care policies.
GPCR ontology: development and application of a G protein-coupled receptor pharmacology knowledge framework
Authors: Przydzial Magdalena J. , Bhhatarai Barun , Koleti Amar , Vempati Uma , Schürer Stephan C. 
Published: September 2013

Abstract
Motivation: Novel tools need to be developed to help scientists analyze large amounts of available screening data with the goal to identify entry points for the development of novel chemical probes and drugs. As the largest class of drug targets, G protein-coupled receptors (GPCRs) remain of particular interest and are pursued by numerous academic and industrial research projects.
Results: We report the first GPCR ontology to facilitate integration and aggregation of GPCR-targeting drugs and demonstrate its application to classify and analyze a large subset of the PubChem database. The GPCR ontology, based on previously reported BioAssay Ontology, depicts available pharmacological, biochemical and physiological profiles of GPCRs and their ligands. The novelty of the GPCR ontology lies in the use of diverse experimental datasets linked by a model to formally define these concepts. Using a reasoning system, GPCR ontology offers potential for knowledge-based classification of individuals (such as small molecules) as a function of the data.
Availability: The GPCR ontology is available at http://www.bioassayontology.org/bao_gpcr and the National Center for Biomedical Ontologies Web site.
Contact: sschurer@med.miami.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
BooleSim: an interactive Boolean network simulator
Authors: Bock Matthias , Scharp Till , Talnikar Chaitanya , Klipp Edda 
Published: September 2013

Abstract
Summary: BooleSim (Boolean network simulator) is an open-source in-browser tool for simulation and manipulation of Boolean networks. It was developed mainly during Google’s Summer of Code 2012 and uses the biographer project for network visualization. It can be used specifically for the modeling of gene regulatory or signal transduction networks.
Availability and implementation: BooleSim is free software and can be downloaded from GitHub (https://github.com/matthiasbock/BooleSim). Online version available at http://rumo.biologie.hu-berlin.de/boolesim/.
Contact: edda.klipp@rz.hu-berlin.de
Changing patterns of cytomegalovirus seroprevalence among pregnant women in Norway between 1995 and 2009 examined in the Norwegian Mother and Child Cohort Study and two cohorts from Sør-Trøndelag County: a cross-sectional study
Authors: Odland Maria Lisa , Strand Kristin M , Nordbø Svein Arne , Forsmo Siri , Austgulen Rigmor , Iversen Ann-Charlotte 
Published: September 2013

ObjectivesTo examine cytomegalovirus (CMV) seroprevalence and associated risk factors for CMV seropositivity in pregnant Norwegian women.DesignCross-sectional study.SettingThe Norwegian Mother and Child Cohort Study (MoBa) in addition to two random samples of pregnant women from Sør-Trøndelag County in Norway.ParticipantsStudy group 1 were 1000 pregnant women, randomly selected among 46 127 pregnancies in the MoBa (1999–2006) at 17/18 week of gestation. Non-ethnic Norwegian women were excluded. Study groups 2 (n=1013 from 1995) and 3 (n=979 from 2009) were pregnant women at 12 weeks of gestation from Sør-Trøndelag County.Outcome measuresCMV seropositivity in blood samples from pregnant Norwegian women.ResultsCMV-IgG antibodies were detected in 59.9% and CMV-IgM antibodies in 1.3% of pregnant Norwegian women in study group 1. Women from North Norway demonstrated a higher CMV-IgG seroprevalence (72.1%) than women from South Norway (58.5%) (OR 1.83, 95% CI 1.17 to 2.88). The CMV-IgG seroprevalence was higher among women with low education (70.5%) compared to women with higher education (OR 2.20, 95% CI 1.24 to 3.90). Between 1995 and 2009 the CMV-IgG seroprevalence increased from 63.1% to 71.4% in pregnant women from Sør-Trøndelag County (study groups 2 and 3; p<0.001). The highest CMV-IgG seroprevalence (79.0%) was observed among the youngest pregnant women (<25 years) from Sør-Trøndelag County in 2009 (study group 3).ConclusionsThe CMV-IgG seroprevalence of pregnant Norwegian women varies with geographic location and educational level. Additionally, the CMV-IgG seroprevalence appears to have increased over the last years, particularly among young pregnant women.
Ten-Eleven Translocation-2 (TET2) Is a Master Regulator of Smooth Muscle Cell Plasticity
Authors: Liu Renjing , Jin Yu , Tang Wai Ho , Qin Lingfeng , Zhang Xinbo , Tellides George , Hwa John , Yu Jun , Martin Kathleen A. 
Published: September 2013

Background—
Smooth muscle cells (SMCs) are remarkably plastic. Their reversible differentiation is required for growth and wound healing but also contributes to pathologies such as atherosclerosis and restenosis. Although key regulators of the SMC phenotype, including myocardin (MYOCD) and KLF4, have been identified, a unifying epigenetic mechanism that confers reversible SMC differentiation has not been reported.

Methods and Results—

Using human SMCs, human arterial tissue, and mouse models, we report that SMC plasticity is governed by the DNA-modifying enzyme ten-eleven translocation-2 (TET2). TET2 and its product, 5-hydroxymethylcytosine (5-hmC), are enriched in contractile SMCs but reduced in dedifferentiated SMCs. TET2 knockdown inhibits expression of key procontractile genes, including
MYOCD
and
SRF
, with concomitant transcriptional upregulation of
KLF4
. TET2 knockdown prevents rapamycin-induced SMC differentiation, whereas TET2 overexpression is sufficient to induce a contractile phenotype. TET2 overexpression also induces SMC gene expression in fibroblasts. Chromatin immunoprecipitation demonstrates that TET2 coordinately regulates phenotypic modulation through opposing effects on chromatin accessibility at the promoters of procontractile versus dedifferentiation-associated genes. Notably, we find that TET2 binds and 5-hmC is enriched in CArG-rich regions of active SMC contractile promoters (
MYOCD
,
SRF
, and
MYH11
). Loss of TET2 and 5-hmC positively correlates with the degree of injury in murine models of vascular injury and human atherosclerotic disease. Importantly, localized TET2 knockdown exacerbates injury response, and local TET2 overexpression restores the 5-hmC epigenetic landscape and contractile gene expression and greatly attenuates intimal hyperplasia in vivo.

Conclusions—
We identify TET2 as a novel and necessary master epigenetic regulator of SMC differentiation.
Comparison of RNA- or LNA-hybrid oligonucleotides in template-switching reactions for high-speed sequencing library preparation
Authors: Harbers Matthias , Kato Sachi , de Hoon Michiel , Hayashizaki Yoshihide , Carninci Piero , Plessy Charles 
Published: September 2013

Abstract

Background
Analyzing the RNA pool or transcription start sites requires effective means to convert RNA into cDNA libraries for digital expression counting. With current high-speed sequencers, it is necessary to flank the cDNAs with specific adapters. Adding template-switching oligonucleotides to reverse transcription reactions is the most commonly used approach when working with very small quantities of RNA even from single cells.

Results
Here we compared the performance of DNA-RNA, DNA-LNA and DNA oligonucleotides in template-switching during nanoCAGE library preparation. Test libraries from rat muscle and HeLa cell RNA were prepared in technical triplicates and sequenced for comparison of the gene coverage and distribution of the reads within transcripts. The DNA-RNA oligonucleotide showed the highest specificity for capped 5′ ends of mRNA, whereas the DNA-LNA provided similar gene coverage with more reads falling within exons.

Conclusions
While confirming the cap-specific preference of DNA-RNA oligonucleotides in template-switching reactions, our data indicate that DNA-LNA hybrid oligonucleotides could potentially find other applications in random RNA sequencing.
The mosaic accessory gene structures of the SXT/R391-like integrative and conjugative elements derived from Vibrio spp. isolated from aquatic products and environment in the Yangtze River estuary, China
Authors: Song Yuze , Yu Pan , Li Bailin , Pan Yingjie , Zhang Xiaojun , Cong Jian , Zhao Yinying , Wang Hua , Chen Lanming 
Published: September 2013

Abstract

Background
The emergence, resurgence and spread of human food-borne pathogenic Vibrios are one of the major contributors to disease burden and mortality particularly in developing countries with disputable sanitary conditions. Previous research on pathogenic Vibrio cholerae and Vibrio parahaemolitycus derived from clinical samples has proposed links between acquisition of virulence and multiple drug resistance traits and intercellular transmissibility of mobile genetic elements in the environment. To date, very few information is available on environmental Vibrio isolates. In this study, we characterized eleven Vibrio strains bearing the SXT/R391-like integrative and conjugative elements (ICEs) derived from aquatic products and environment in the Yangtze River Estuary, China.

Results
The eleven Vibrio strains were isolated in 2010 to 2011, and taxonomically identified, which included six Vibrio cholerae, three Vibrio parahaemolyticus, one Vibrio alginolyticus and one Vibrio natriegens. Most of the strains displayed strong resistance phenotypes to ampicillin, mercury and chromium. The majority of their ICEs, which belong to S and R exclusion system groups, contain ICEs-chromosome junction sequences and highly conserved core-genes required for ICE transfer. However, comparative sequence analysis uncovered interesting diversity in their mosaic accessory gene structures, which carry many novel genes that have not been described in any known ICEs to date. In addition, antibiotic resistance was transmitted by ICEVchChn6 and ICEVpaChn1 from V. cholerae, V. parahaemolyticus to E. coli MG1655 via conjugation, respectively. Our data also revealed that the ICEs characterized in this study are phylogenetically distant from most of the SXT/R391 ICEs reported previously, which may represent a novel cluster likely shaped by the ecological environment in the Yangtze River Estuary, China.

Conclusions
This study constitutes the first investigation of ICEs-positive Vibrio spp. in the Yangze River Estuary, China. The newly identified ICEs were characterized with mosaic accessory gene structures and many novel genes. The results demonstrated self-transmissibility of antibiotic resistance mediated by two of the ICEs from V. cholerae, V. parahaemolyticus to E. coli via conjugation, respectively. Our results also revealed that the ICEs examined in this study may represent a novel cluster in the SXT/R391 family.
Identification and fine-mapping of a QTL, qMrdd1, that confers recessive resistance to maize rough dwarf disease
Authors: Tao Yongfu , Liu Qingcai , Wang Honghong , Zhang Yanjun , Huang Xinyi , Wang Baobao , Lai Jinsheng , Ye Jianrong , Liu Baoshen , Xu Mingliang 
Published: September 2013

Abstract

Background
Maize rough dwarf disease (MRDD) is a devastating viral disease that results in considerable yield losses worldwide. Three major strains of virus cause MRDD, including maize rough dwarf virus in Europe, Mal de Río Cuarto virus in South America, and rice black-streaked dwarf virus in East Asia. These viral pathogens belong to the genus fijivirus in the family Reoviridae. Resistance against MRDD is a complex trait that involves a number of quantitative trait loci (QTL). The primary approach used to minimize yield losses from these viruses is to breed and deploy resistant maize hybrids.

Results
Of the 50 heterogeneous inbred families (HIFs), 24 showed consistent responses to MRDD across different years and locations, in which 9 were resistant and 15 were susceptible. We performed trait-marker association analysis on the 24 HIFs and found six chromosomal regions which were putatively associated with MRDD resistance. We then conducted QTL analysis and detected a major resistance QTL, qMrdd1, on chromosome 8. By applying recombinant-derived progeny testing to self-pollinated backcrossed families, we fine-mapped the qMrdd1 locus into a 1.2-Mb region flanked by markers M103-4 and M105-3. The qMrdd1 locus acted in a recessive manner to reduce the disease-severity index (DSI) by 24.2–39.3%. The genetic effect of qMrdd1 was validated using another F6 recombinant inbred line (RIL) population in which MRDD resistance was segregating and two genotypes at the qMrdd1 locus differed significantly in DSI values.

Conclusions
The qMrdd1 locus is a major resistance QTL, acting in a recessive manner to increase maize resistance to MRDD. We mapped qMrdd1 to a 1.2-Mb region, which will enable the introgression of qMrdd1-based resistance into elite maize hybrids and reduce MRDD-related crop losses.
Relationship between polymorphisms in vitamin D metabolism-related genes and the risk of rickets in Han Chinese children
Authors: Zhang Yuling , Yang Shufen , Liu Ye , Ren Lihong 
Published: September 2013

Abstract

Background
Vitamin D deficiency rickets is common in China. Genetic factors may play an important role in the susceptibility to rickets. Our study aimed to identify the relationship between three vitamin D-related genes (group specific component [GC], cytochrome P450, family 2, subfamily R, polypeptide 1 (CYP2R1), and 7-dehydrocholesterol reductase/nicotinamide-adenine dinucleotide synthetase 1 (DHCR7/NADSYN1) and rickets in Han Chinese children from northeastern China.

Methods
A total of 506 Han children from northeastern China were enrolled in the current study. Twelve SNPs in three candidate genes were genotyped using the SNaPshot assay. Linear regression was used to examine the effect of 12 single-nucleotide polymorphisms (SNPs) on the risk of rickets.

Results
In our case–control cohort, six alleles of the 12 SNPs conferred a significantly increased risk of rickets in GC (rs4588 C, P = 0.003, OR: 0.583, 95% CI: 0.412-0.836; rs222020 C, P = 0.009, OR: 1.526, 95% CI: 1.117-2.0985; rs2282679 A, P = 0.010, OR: 0.636, 95% CI: 0.449-0.900; and rs2298849 C, P = 0.001, OR: 1.709, 95% CI: 1.250-2.338) and in CYP2R1 (rs10741657 G, P = 0.019, OR: 1.467, 95% CI: 1.070-2.011; and rs2060793 G, P = 0.023, OR: 0.689, 95% CI: 0.502-0.944). The results remained significant after adjustment for sex and body mass index. We further analyzed the effect of genotypes under three different genetic models. After using Bonferroni’s method for multiple corrections, rs4588, rs2282679, and rs2298849 of the GC gene were significantly associated with rickets under the dominant (P =0.003 for rs4588, P =0.024 for rs2282679, and P =0.005 for rs2298849) and additive models (P = 0.006 for rs4588, P = 0.024 for rs2282679, and P = 0.005 for rs2298849). Haplotype analysis showed that the CAT haplotype of the GC gene (P = 0.005) and the GAA haplotype of the CYP2R1 gene (P = 0.026) were associated with susceptibility to rickets.

Conclusions
This case–control study confirmed the strong effect of GC and CYP2R1 loci on rickets in Han children from northeastern China.