bluuebunny/crossref_metadata_2025_split huggingface dataset:
Left atrial extension of hepatoblastoma via left superior pulmonary vein
Authors: Atalay Atakan , Gocen Uğur , Yaliniz Hafize 
Published: November 2013

AbstractHepatoblastoma is the most common malignant liver tumour in early childhood. The metastatic extension of hepatoblastoma into the left atrium via the pulmonary vein is rare. Reported lesions almost always involve a right-sided approach. Here we report the case of a 3-year-old girl with a recurrent hepatoblastoma at multiple sites, including the left atrium, brain, and lung. The patient was treated surgically for the prevention of further embolic complications and cardiac failure.
Onset and temporal sequencing of lifetime anxiety, mood and substance use disorders in the general population
Authors: Slade T. , McEvoy P. M. , Chapman C. , Grove R. , Teesson M. 
Published: November 2013

Aims.To date, very few studies have examined the bi-directional associations between mood disorders (MDs), anxiety disorders (ADs) and substance use disorders (SUDs), simultaneously. The aims of the current study were to determine the rates and patterns of comorbidity of the common MDs, ADs and SUDs and describe the onset and temporal sequencing of these classes of disorder, by sex.Methods.Data came from the 2007 Australian National Survey of Mental Health and Wellbeing, a nationally representative household survey with 8841 (60% response rate) community residents aged 16–85.Results.Pre-existing mental disorders increase the risk of subsequent mental disorders in males and females regardless of the class of disorder. Pre-existing SUDs increase the risk of subsequent MDs and ADs differentially for males and females. Pre-existing MDs increase the risk of subsequent ADs differentially for males and females.Conclusions.Comorbidity remains a significant public health issue and current findings point to the potential need for sex-specific prevention and treatment responses.
Think Manager – Think Male in Adolescents and its Relation to Sexism and Emotions in Leadership
Authors: García-Ael Cristina , Cuadrado Isabel , Molero Fernando 
Published: November 2013

AbstractFrom the perspective of the Think manager – Think male, this study was conducted to examine the type of leadership role depending on gender in a sample of 158 Spanish adolescents –according to three types of leaders: “male middle leader”, “female middle leader” and “middle leader in general”. The kind of emotional expression (positive and negative) evoked by their leadership behaviors (task– and relationship– oriented) was also analyzed. Lastly, whether adolescents’ sexist beliefs affected the attribution of traits and the emotional expression towards these leaders was examined. Results showed that task-oriented traits were more characteristic of the leadership role than relationship-oriented traits. Adolescents expressed more positive emotions towards a task-oriented leader and towards a leader behaving in ways associated with both task– and relationship– oriented styles, but only for men. Finally, hostile sexism predicted fewer task-oriented traits to female leaders, more negative affect towards task-oriented male leaders and towards counter-stereotypic leaders. These results were moderated by the sex of adolescents.
Insights into the evolution of divergent nucleotide-binding mechanisms among pseudokinases revealed by crystal structures of human and mouse MLKL
Authors: Murphy James M. , Lucet Isabelle S. , Hildebrand Joanne M. , Tanzer Maria C. , Young Samuel N. , Sharma Pooja , Lessene Guillaume , Alexander Warren S. , Babon Jeffrey J. , Silke John , Czabotar Peter E. 
Published: November 2013

The pseudokinase MLKL (mixed lineage kinase domain-like) was identified recently as an essential checkpoint in the programmed necrosis or ‘necroptosis’ cell death pathway. In the present study, we report the crystal structure of the human MLKL pseudokinase domain at 1.7 Å (1 Å=0.1 nm) resolution and probe its nucleotide-binding mechanism by performing structure-based mutagenesis. By comparing the structures and nucleotide-binding determinants of human and mouse MLKL orthologues, the present study provides insights into the evolution of nucleotide-binding mechanisms among pseudokinases and their mechanistic divergence from conventional catalytically active protein kinases.
The Benefits of Spatially Differentiated Regulation: The Response to Acid Rain by U.S. States Prior to the Acid Rain Program
Authors: Perino Grischa , Talavera Olena 
Published: November 2013

AbstractLocation is a crucial driver of both the marginal abatement and damage costs of sulfur dioxide emissions by U.S. coal‐fired power plants. Before the start of the Acid Rain Program in 1995, old boilers were subject to emission rate standards set by individual states. We investigate how individual states adjusted their sulfur regulation laws in response to acid rain, and whether they accounted for differences in marginal abatement costs, vulnerability to agricultural damages, special industry interests, or inter‐state externalities. The welfare gain compared to a uniform reduction in emission rate standards is estimated to be $21 million (in 1995 dollars) annually.
PhosphoNetworks: a database for human phosphorylation networks
Authors: Hu Jianfei , Rho Hee-Sool , Newman Robert H. , Zhang Jin , Zhu Heng , Qian Jiang 
Published: November 2013

Abstract
Summary: Phosphorylation plays an important role in cellular signal transduction. Current phosphorylation-related databases often focus on the phosphorylation sites, which are mainly determined by mass spectrometry. Here, we present PhosphoNetworks, a phosphorylation database built on a high-resolution map of phosphorylation networks. This high-resolution map of phosphorylation networks provides not only the kinase–substrate relationships (KSRs), but also the specific phosphorylation sites on which the kinases act on the substrates. The database contains the most comprehensive dataset for KSRs, including the relationships from a recent high-throughput project for identification of KSRs using protein microarrays, as well as known KSRs curated from the literature. In addition, the database also includes several analytical tools for dissecting phosphorylation networks. PhosphoNetworks is expected to play a prominent role in proteomics and phosphorylation-related disease research.
Availability and implementation: http://www.phosphonetworks.org
Contact: jiang.qian@jhmi.edu
CheNER: chemical named entity recognizer
Authors: Usié Anabel , Alves Rui , Solsona Francesc , Vázquez Miguel , Valencia Alfonso 
Published: November 2013

Abstract
Motivation: Chemical named entity recognition is used to automatically identify mentions to chemical compounds in text and is the basis for more elaborate information extraction. However, only a small number of applications are freely available to identify such mentions. Particularly challenging and useful is the identification of International Union of Pure and Applied Chemistry (IUPAC) chemical compounds, which due to the complex morphology of IUPAC names requires more advanced techniques than that of brand names.
Results: We present CheNER, a tool for automated identification of systematic IUPAC chemical mentions. We evaluated different systems using an established literature corpus to show that CheNER has a superior performance in identifying IUPAC names specifically, and that it makes better use of computational resources.
Availability and implementation: http://metres.udl.cat/index.php/9-download/4-chener, http://chener.bioinfo.cnio.es/
Contact: miguel.vazquez@cnio.es
Supplementary information: Supplementary data are available at Bioinformatics online.
ClockstaR: choosing the number of relaxed-clock models in molecular phylogenetic analysis
Authors: Duchêne Sebastián , Molak Martyna , Ho Simon Y. W. 
Published: November 2013

Abstract
Summary: Relaxed molecular clocks allow the phylogenetic estimation of evolutionary timescales even when substitution rates vary among branches. In analyses of large multigene datasets, it is often appropriate to use multiple relaxed-clock models to accommodate differing patterns of rate variation among genes. We present ClockstaR, a method for selecting the number of relaxed clocks for multigene datasets.
Availability: ClockstaR is freely available for download at http://sydney.edu.au/science/biology/meep/software/.
Contact: sebastian.duchene@sydney.edu.au
Supplementary information: Supplementary data are available at Bioinformatics online.
α-Actinin-3 deficiency alters muscle adaptation in response to denervation and immobilization
Authors: Garton F.C. , Seto J.T. , Quinlan K.G.R. , Yang N. , Houweling P.J. , North K.N. 
Published: November 2013

Abstract
Homozygosity for a common null polymorphism (R577X) in the ACTN3 gene results in the absence of the fast fibre-specific protein, α-actinin-3 in ∼16% of humans worldwide. α-Actinin-3 deficiency is detrimental to optimal sprint performance and benefits endurance performance in elite athletes. In the general population, α-actinin-3 deficiency is associated with reduced muscle mass, strength and fast muscle fibre area, and poorer muscle function with age. The Actn3 knock-out (KO) mouse model mimics the human phenotype, with fast fibres showing a shift towards slow/oxidative metabolism without a change in myosin heavy chain (MyHC) isoform. We have recently shown that these changes are attributable to increased activity of the calcineurin-dependent signalling pathway in α-actinin-3 deficient muscle, resulting in enhanced response to exercise training. This led us to hypothesize that the Actn3 genotype influences muscle adaptation to disuse, irrespective of neural innervation. Separate cohorts of KO and wild-type mice underwent 2 weeks immobilization and 2 and 8 weeks of denervation. Absence of α-actinin-3 resulted in reduced atrophic response and altered adaptation to disuse, as measured by a change in MyHC isoform. KO mice had a lower threshold to switch from the predominantly fast to a slower muscle phenotype (in response to immobilization) and a higher threshold to switch to a faster muscle phenotype (in response to denervation). We propose that this change is mediated through baseline alterations in the calcineurin signalling pathway of Actn3 KO muscle. Our findings have important implications for understanding individual responses to muscle disuse/disease and training in the general population.
Fibroblast Growth Factor Receptor Two (FGFR2) Regulates Uterine Epithelial Integrity and Fertility in Mice
Authors: Filant Justyna , DeMayo Franco J. , Pru James K. , Lydon John P. , Spencer Thomas E. 
Published: November 2013

AbstractFibroblast growth factors (FGFs) and their receptors (FGFRs) regulate luminal epithelial (LE) cell proliferation in the adult mouse uterus. This study tested the hypothesis that FGFR2 has a biological role in postnatal development and function of the uterus by conditionally deletingFgfr2 after birth using progesterone receptor (Pgr)-Cre mice. AdultFgfr2 mutant female mice were initially subfertile and became infertile with increasing parity. No defects in uterine gland development were observed in conditionalFgfr2 mutant mice. In the adult,Fgfr2 mutant mice possessed a histologically normal reproductive tract with the exception of the uterus. The LE of theFgfr2 mutant uterus was stratified, but no obvious histological differences were observed in the glandular epithelium, stroma, or myometrium. Within the stratified LE, cuboidal basal cells were present and positive for basal cell markers (KRT14 and TRP63). Nulliparous bredFgfr2 mutants contained normal numbers of blastocysts on Day 3.5 postmating, but the number of embryo implantation sites was substantially reduced on Day 5.5 postmating. These results support the idea that loss of FGFR2 in the uterus after birth alters its development, resulting in LE stratification and peri-implantation pregnancy loss.
Incidence of Legionella and heterotrophic bacteria in household rainwater tanks in Azumino, Nagano prefecture, Japan
Authors: Kobayashi Michiko , Oana Kozue , Kawakami Yoshiyuki 
Published: November 2013

ABSTRACTMany administrative agencies in Japan are encouraging installation of household rainwater‐storage tanks for more effective use of natural rainwater. Water samples were collected periodically from 43 rainwater tanks from 40 households and tested for the presence of Legionella species and the extent of heterotrophic bacteria in Azumino city, Nagano prefecture, Japan. PCR assays indicated the presence of Legionella spp. in 12 (30%) of the 43 tank water samples. Attempts were made to identify correlations between PCR positive samples, topography, pH, chemical oxygen demand (COD), atmospheric temperature and the numbers of heterotrophic bacteria. Between June and October, 2012, the numbers of heterotrophic bacteria in rainwater tanks and the values of COD positively correlated with the presence of Legionella species. In most of the Legionella‐positive cases, heterotrophic bacterial cell counts were >104 CFU/mL. Moreover, Legionella species were less frequently detected when the COD value was >5 mg KMnO4/L. Therefore, at least in Azumino, Japan between June and October 2012, both heterotrophic bacterial counts and COD values may be considered index parameters for the presence of Legionella cells in rainwater tanks. Much more accumulation of such data is needed to verify the accuracy of these findings.
Halomonas sulfidaeris‐dominated microbial community inhabits a 1.8 km‐deep subsurface Cambrian Sandstone reservoir
Authors: Dong Yiran , Kumar Charu Gupta , Chia Nicholas , Kim Pan‐Jun , Miller Philip A. , Price Nathan D. , Cann Isaac K. O. , Flynn Theodore M. , Sanford Robert A. , Krapac Ivan G. , Locke Randall A. , Hong Pei‐Ying , Tamaki Hideyuki , Liu Wen‐Tso , Mackie Roderick I. , Hernandez Alvaro G. , Wright Chris L. , Mikel Mark A. , Walker Jared L. , Sivaguru Mayandi , Fried Glenn , Yannarell Anthony C. , Fouke Bruce W. 
Published: November 2013

SummaryA low‐diversity microbial community, dominated by the γ‐proteobacterium Halomonas sulfidaeris, was detected in samples of warm saline formation porewater collected from the Cambrian Mt. Simon Sandstone in the Illinois Basin of the North American Midcontinent (1.8 km/5872 ft burial depth, 50°C, pH 8, 181 bars pressure). These highly porous and permeable quartz arenite sandstones are directly analogous to reservoirs around the world targeted for large‐scale hydrocarbon extraction, as well as subsurface gas and carbon storage. A new downhole low‐contamination subsurface sampling probe was used to collect in situ formation water samples for microbial environmental metagenomic analyses. Multiple lines of evidence suggest that this H. sulfidaeris‐dominated subsurface microbial community is indigenous and not derived from drilling mud microbial contamination. Data to support this includes V1‐V3 pyrosequencing of formation water and drilling mud, as well as comparison with previously published microbial analyses of drilling muds in other sites. Metabolic pathway reconstruction, constrained by the geology, geochemistry and present‐day environmental conditions of the Mt. Simon Sandstone, implies that H. sulfidaeris‐dominated subsurface microbial community may utilize iron and nitrogen metabolisms and extensively recycle indigenous nutrients and substrates. The presence of aromatic compound metabolic pathways suggests this microbial community can readily adapt to and survive subsurface hydrocarbon migration.
Out of the body: embodiment and its vicissitudes
Authors: Connolly Angela 
Published: November 2013

AbstractBody‐mind dualism and the consequent neglect of the body of the analyst can have important negative effects on the analytical process leading all too often to misinterpretations of the analysand's verbal and non‐verbal communications and to disturbances of analytical temporality. This is intensified when we are dealing with individuals where disembodiment and states of psychic deadness are central features. The paper explores the philosophical roots of the idea of a disembodied mind and the way in which this impacts our relationship with the world. While André Green's concept of the dead mother and disturbances in the sense of self‐agency have been held to play an important role in states of psychic deadness, I suggest that it is rather disturbances in the sense of body ownership and of the body image which are more central. The paper then discusses the particular kinds of countertransference that can be evoked in the analyst when we find ourselves dealing with this type of patient and suggests how we can use our embodied countertransference to become aware of and elaborate our own feelings of deadness in order to overcome the loss of temporality that is characteristic of such states. This is illustrated with reference to my work with a young man with a masochistic perversion and a severe disturbance of the body image with an accompanying profound sense of psychic deadness.
James Astor in conversation with Warren Colman
Authors: Astor James , Colman Warren 
Published: November 2013

AbstractIn this interview with Warren Colman, James Astor speaks about his development as a Jungian analyst from his own experience of personal analysis in the 1960s to his recent retirement from clinical practice. The discussion covers his long association with Michael Fordham, the child analytic training at the SAP, the infant observation seminars with Fordham and Gianna Henry through which Fordham was able to make new discoveries about infant development, his experience of supervision with Donald Meltzer and the development of his own thinking through a series of papers on the analytic process, supervision and the relation between language and truth. The interview concludes with reflections about the legacy of Michael Fordham and the future of analytic work.
The safety of combined sedation with propofol plus fentanyl for endoscopy screening and endoscopic variceal ligation in cirrhotic patients
Authors: MAO Wei , WEI Xiu Qing , TAO Jin , ZHEN Feng Ping , WEN Zhuo Fu , WU Bin 
Published: November 2013

ObjectiveWe aimed to investigate the safety of combined sedation with propofol plus fentanyl in patients with liver cirrhosis during screening esophagogastroduodenoscopy (SEGD) and a secondary prophylaxis for esophageal varices, endoscopic gastrointestinal ligation (EVL).MethodsA total of 309 patients with liver cirrhosis were enrolled and divided into the sedated SEGD group (n = 83), the sedated EVL group (n = 137) and the conscious EVL group (n = 89), respectively, and 100 participants with no liver diseases who underwent endoscopy for gastritis were regarded as the sedated control group. Patients in the sedated groups were administrated with propofol plus fentanyl during the endoscopic procedures and their minimal hepatic encephalopathy and sedation‐related complications, including aspiration, hypoxia, hypotension and bradycardia, were evaluated and compared. The assessments of patient satisfaction and patient cooperation in the sedated and the conscious EVL groups were conducted.ResultsThe incidences of complications during the endoscopic procedures were not significantly different among the sedated groups (20.5% in the sedated SEGD group, 22.6% in the sedated EVL group and 19.0% in the sedated control group). No minimal hepatic encephalopathy was induced in the sedated groups. More patients in the sedated EVL group were satisfactory with the procedure compared with the conscious EVL group, as evaluated by both endoscopists and the cirrhotic patients.ConclusionsA combined sedation with propofol plus fentanyl is safe for EVL as well as for SEGD in cirrhotic patients. Sedation might make it easier for endoscopists to perform procedures and might be more acceptable for cirrhotic patients.
Vegetation dynamics under variable conditions in the famous sandy steppe of southern Tunisia
Authors: Attia Wassim , Tarhouni Mohamed , Ouled Belgacem Azaiez , Gammar Omar , Khatteli Houcine 
Published: November 2013

AbstractDuring last decades, the natural vegetation cover in southern Tunisia, mainly dominated by dwarf and sparse shrub, was continuously disturbed under various human activities especially on sandy soil (easily eroded). The ecological characteristics (soil structure and texture, vegetation, topography…) of sandy steppes, with Rhanterium suaveolens Desf., enhanced their sharp decline. This study aims to investigate the vegetation status of two R. suaveolens steppes (R: protected; r: degraded) under different conditions in five sites belonging to southern Tunisia using the quadrat point method and some ecological indicators. Main results show that vegetation cover is related to climatic conditions. Plant density is mainly affected by rainfall and human activities. The annual and perennial density and cover are high during the rainy season (spring) compared with the dry one (fall). The degraded steppes (r) are mainly dominated by annual plants but the protected steppes (R) contain more perennials. This work can be very useful for the sustainable sandy steppes management under different stress and human disturbances in dry area. It presents a great national and international importance (economic, social, nature conservation…) such as job creation and limiting rural exodus.
Fertility and sexual function in long‐term survivors of haematological malignancy: using patient‐reported outcome measures to assess a neglected area of need in the late effects clinic
Authors: Greaves Paul , Sarker Shah‐Jalal , Chowdhury Kashfia , Johnson Rachel , Matthews Janet , Matthews Rebecca , Smith Matthew , Korszun Ania , Gribben John G. , Lister T. Andrew 
Published: November 2013

SummaryProblems of sexual function and fertility in long‐term survivors (≥5 years) of haematological malignancy are often neglected in clinic. Our centre carried out a questionnaire study in this population addressing patient‐perceived fertility and sexual function. 718 patients responded (56% of those invited; 39% Hodgkin, 45% non‐Hodgkin lymphoma, 16% acute leukaemia). Respondent women were more likely to remain childless than a normal control population. Self‐reported infertility was more likely in men than women [odds ratio (OR) 1·77, P = 0·001]. Myeloablative therapy increased the likelihood of childlessness (OR 2·48, P = 0·004). Few attended fertility support services (12%). 24% of men banked sperm and 29% of these used the sample, of which 46% resulted in successful pregnancy. Fertility clinic attendance and sperm storage was more likely post‐1990 (OR 4·05, P < 0·001; OR 5·05, P < 0·001 respectively). Reporting a negative impact of cancer on sexual function was more common in women than men (OR 2·20, P < 0·001), and increased with current age and age at diagnosis (by 3–4% per year, P ≤ 0·001) but decreased with longer follow‐up (by 2%/year, P = 0·005). Patients on anti‐depressants and those reporting cancer‐related body change/appearance concerns more frequently reported a negative impact (P < 0·04 and P < 0·03 respectively). These self‐reported outcomes confirm literature findings, suggest improvement over time, but highlight a need for involvement of support services.
A model of advertising format competition: on the use of celebrities in ads
Authors: Clark C. Robert , Horstmann Ignatius J. 
Published: November 2013

AbstractWe develop a model that endogenizes both advertising format – ads with or without celebrity endorsements – and the endorsement fee. Marketing studies suggest that celebrities enhance brand recall and perception of product value. In our model, ads featuring celebrities occur when the product market is large – endorsements are likely for products sold nationally – and when products are sufficiently similar that the persuasive character of advertising looms large in demand – running shoes, beauty products, soft drinks, for example. Celebrity endorsement fees are increasing in market size and in the degree of similarity of the products being advertised.