bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Discrete Prognostic Groups in Ewing Sarcoma
Authors: Karski Erin E. , McIlvaine Elizabeth , Segal Mark R. , Krailo Mark , Grier Holcombe E. , Granowetter Linda , Womer Richard B. , Meyers Paul A. , Felgenhauer Judy , Marina Neyssa , DuBois Steven G. 
Published: August 2015

BackgroundAlthough multiple prognostic variables have been proposed for Ewing sarcoma (EWS), little work has been done to further categorize these variables into prognostic groups for risk classification.ProcedureWe derived initial prognostic groups from 2,124 patients with EWS in the SEER database. We constructed a multivariable recursive partitioning model of overall survival using the following covariates: age; stage; race/ethnicity; sex; axial primary; pelvic primary; and bone or soft tissue primary. Based on this model, we identified risk groups and estimated 5‐year overall survival for each group using Kaplan–Meier methods. We then applied these groups to 1,680 patients enrolled on COG clinical trials.ResultsA multivariable model identified five prognostic groups with significantly different overall survival: (i) localized, age <18 years, non‐pelvic primary; (ii) localized, age <18, pelvic primary or localized, age ≥18, white, non‐Hispanic; (iii) localized, age ≥18, all races/ethnicities other than white, non‐Hispanic; (iv) metastatic, age <18; and (v) metastatic, age ≥18. These five groups were applied to the COG dataset and showed significantly different overall and event‐free survival based upon this classification system (P < 0.0001). A sub‐analysis of COG patients treated with ifosfamide and etoposide as a component of therapy evaluated these findings in patients receiving contemporary therapy.ConclusionsRecursive partitioning analysis yields discrete prognostic groups in EWS that provide valuable information for patients and clinicians in determining an individual patient's risk of death. These groups may enable future clinical trials to adjust EWS treatment according to individualized risk. Pediatr Blood Cancer © 2015 Wiley Periodicals, Inc.
The importance of emotional intelligence and meaning in life in psycho‐oncology
Authors: Teques Andreia Pereira , Carrera Glória Bueno , Ribeiro José Pais , Teques Pedro , Ramón Ginés Llorca 
Published: August 2015

AbstractObjectiveCancer was considered the disease of the 20th century, and the management, treatment, and adaptation of patients to general wellbeing were worldwide concerns. Emotional intelligence has frequently been associated with wellbeing and considered one important factor to optimal human functioning. The purpose of the present study was to test the differences regarding the relationship between emotional intelligence, purpose in life, and satisfaction with life between cancer and healthy people.MethodsThis model was tested using structural path analysis in two independent samples. First, in a general Portuguese population without chronic disease, 214 participants (nmale = 41, nfemale = 173; Mage = 53). Second, in 202 patients with cancer (nmale = 40, nfemale = 162; Mage = 58.65). A two‐step methodology was used to test the research hypothesis.ResultsFirst, a confirmatory factor analysis supported the measurement model. All factors also show reliability, convergent, and discriminate validity. Second, the path coefficients for each model indicate that the proposed relationships differ significantly according to the groups. The perception capacities of emotional intelligence were more related to satisfaction with life and purpose in life in oncologic patients than in the general population without chronic disease, specifically emotional understanding and regulation. Likewise, the relationship between purpose in life and satisfaction with life in oncologic patients was significantly higher than for the general population.ConclusionThe current findings thus suggest that emotional intelligence and purpose in life are potential components to promoting satisfaction in life in healthy people and more so in oncologic patients. Copyright © 2015 John Wiley & Sons, Ltd.
Dexippus and the Gothic Invasions: Interpreting the New Vienna Fragment (Codex Vindobonensis Hist. gr.73, ff. 192v–193r)
Authors: Mallan Christopher , Davenport Caillan 
Published: August 2015

ABSTRACTThis article presents an English translation and analysis of a new historical fragment, probably from Dexippus’Scythica, published by Gunther Martin and Jana Grusková in 2014. The fragment, preserved in a palimpsest in the Austrian National Library, describes a Gothic attack on Thessalonica and the subsequent preparations of the Greeks to repel the barbarian force as it moved south into Achaia. The new text provides several important details of historical, prosopographical and historiographical significance, which challenge both our existing understanding of the events in Greece during the reign of Gallienus and the reading of the main literary sources for this period. In this article we look to secure the Dexippan authorship of the fragment, identify the individuals named in the text, and date the events described in the text to the early 260sa.d.
FromTopostoOikos: The Standardization of Glass Containers as Epistemic Boundaries in Modern Laboratory Research (1850–1900)
Authors: Espahangizi Kijan 
Published: August 2015

ArgumentGlass vessels such as flasks and test tubes play an ambiguous role in the historiography of modern laboratory research. In spite of the strong focus on the role of materiality in the last decades, the scientific glass vessel – while being symbolically omnipresent – has remained curiously neglected in regard to its materiality. The popular image ortoposof the transparent, neutral, and quasi-immaterial glass container obstructs the view of the physico-chemical functionality of this constitutive inner boundary in modern laboratory environments and its material historicity. In order to understand how glass vessels were able to provide a stable epistemic containment of spatially enclosed experimental phenomena in the new laboratory ecologies emerging in the nineteenth and early twentieth century, I will focus on the history of thematerialstandardization of laboratory glassware. I will follow the rise of a new awareness for measurement errors due to the chemical agency of experimental glass vessels, then I will sketch the emergence of a whole techno-scientific infrastructure for the improvement of glass container quality in late nineteenth-century Germany. In the last part of my argument, I will return to the laboratory by looking at the implementation of this glass reform that created a newoikosfor the inner experimental milieus of modern laboratory research.
Relation of intelligence quotient and body mass index in preschool children: a community-based cross-sectional study
Authors: Tabriz A A , Sohrabi M-R , Parsay S , Abadi A , Kiapour N , Aliyari M , Ahmadi F , Roodaki A 
Published: August 2015

AbstractObjective:Overweight and obesity in children is a global problem. Besides physical effects, obesity has harmful psychological effects on children.Methods:We carried out cross-sectional community-based study to investigate the relation between body mass index (BMI) and cognitive functioning in preschool children. Thirteen socioeconomical elements of 1151 children were measured and analyzed based on their intelligence quotient (IQ) test results. Thirteen out of 33 provinces were selected randomly, and schools were selected as clusters in rural and urban areas. Descriptive statistics,t-test, analysis of variance and regression were used when appropriate.Results:Our analysis showed that IQ was associated with household income, place of residence, delivery type, type of infant feeding and father’s and mother’s education level (P<0.001 for all). Using penalized linear regression for eliminating the impact of confounding factor, our study shows that, living in metropolitan (β=2.411) and urban areas (β=2.761), the level of participants’ father's education (β=5.251) was positively and BMI (β=−0.594) was negatively related with IQ test results.ConclusionsThe findings of the present study showed that a lower IQ score is associated with higher BMI. However, this relation appears to be largely mediated when the socioeconomic status was considered.
DNA sequencing with MspA: Molecular Dynamics simulations reveal free-energy differences between sequencing and non-sequencing mutants
Authors: Manara Richard M.A. , Jayne Wallace E. , Khalid Syma 
Published: August 2015

AbstractMspA has been identified as a promising candidate protein as a component of a nanopore-based DNA-sequencing device. However the wildtype protein must be engineered to incorporate all of the features desirable for an accurate and efficient device. In the present study we have utilized atomistic molecular dynamics to perform umbrella-sampling calculations to calculate the potential of mean force (PMF) profiles for translocation of the four DNA nucleotides through MspA. We show there is an energetic barrier to translocation of individual nucleotides through a mutant that closely resembles the wildtype protein, but not through a mutant engineered for the purpose of sequencing. Crucially we are able to quantify the change in free energy for mutating key residues. Thus providing a quantitative characterisation of the energetic impact of individual amino acid sidechains on nucleotide translocation through the pore of MspA.
Subalpine Pyrenees received higher nitrogen deposition than predicted by EMEP and CHIMERE chemistry-transport models
Authors: Boutin Marion , Lamaze Thierry , Couvidat Florian , Pornon André 
Published: August 2015

AbstractDeposition of reactive nitrogen (N) from the atmosphere is expected to be the third greatest driver of biodiversity loss by the year 2100. Chemistry-transport models are essential tools to estimate spatially explicit N deposition but the reliability of their predictions remained to be validated in mountains. We measured N deposition and air concentration over the subalpine Pyrenees. N deposition was found to range from 797 to 1,463 mg N m−2 year−1. These values were higher than expected from model predictions, especially for nitrate, which exceeded the estimations of EMEP by a factor of 2.6 and CHIMERE by 3.6. Our observations also displayed a reversed reduced-to-oxidized ratio in N deposition compared with model predictions. The results highlight that the subalpine Pyrenees are exposed to higher levels of N deposition than expected according to standard predictions and that these levels exceed currently recognized critical loads for most high-elevation habitats. Our study reveals a need to improve the evaluation of N deposition in mountains which are home to a substantial and original part of the world’s biodiversity.
Properties and mechanism of action of pyruvate, phosphate dikinase from leaves
Authors: Andrews T. J. , Hatch M. D. 
Published: August 2015

1. Sugar-cane leaf pyruvate,Pi dikinase was prepared free of enzymes that would interfere with studies on the stoicheiometry and mechanism of the reaction it catalyses. The reaction was unequivocally shown to involve the conversion of equimolar amounts of pyruvate, ATP and Pi into phosphoenolpyruvate, AMP and PPi. 2. The purified enzyme was stable at pH8·3 only if stored at about 20° in the presence of Mg2+ and a thiol-reducing reagent, care being taken to prevent the oxidation of the thiol. 3. The apparent Michaelis constants for phosphoenolpyruvate and PPi were 0·11mm and 0·04mm respectively and that for AMP was less than 4μm. 4. At pH8·3 the initial velocity of the reaction was about 6 times as fast in the direction towards phosphoenolpyruvate synthesis as in the reverse direction. 5. With the exception of ATP, all the products of the reaction in both directions were inhibitory. 6. The phosphate groups of PPi were derived from Pi and from the terminal phosphate of ATP. 7. Isotope-exchange studies indicated that the reaction proceeds in the following steps:
Enzyme+ATP+Pi ⇌ Enzyme–P+AMP+PPi
Enzyme–P+pyruvate ⇌ Enzyme+phosphoenolpyruvate
Runx3 negatively regulates Osterix expression in dental pulp cells
Authors: Zheng Li , Iohara Koichiro , Ishikawa Masaki , Into Takeshi , Takano-Yamamoto Teruko , Matsushita Kenji , Nakashima Misako 
Published: August 2015

Osterix, a zinc-finger-containing transcription factor, is required for osteoblast differentiation and bone formation. Osterix is also expressed in dental mesenchymal cells of the tooth germ. However, transcriptional regulation by Osterix in tooth development is not clear. Genetic studies in osteogenesis place Osterix downstream of Runx2 (Runt-related 2). The expression of Osterix in odontoblasts overlaps with Runx3 during terminal differentiation in vivo. Runx3 down-regulates Osterix expression in mouse DPCs (dental pulp cells). Therefore the regulatory role of Runx3 on Osterix expression in tooth development was investigated. Enforced expression of Runx3 down-regulated the activity of the Osterix promoter in the human embryonic kidney 293 cell line. When the Runx3 responsive element on the Osterix promoter, located at −713 to −707 bp (site 3, AGTGGTT) relative to the cap site, was mutated, this down-regulation was abrogated. Furthermore, electrophoretic mobility-shift assay and chromatin immunoprecipitation assays in mouse DPCs demonstrated direct functional binding of Runx3 to the Osterix promoter. These results demonstrate the transcriptional regulation of Osterix expression by Runx3 during differentiation of dental pulp cells into odontoblasts during tooth development.
Dual-specificity phosphatases: critical regulators with diverse cellular targets
Authors: Patterson Kate I. , Brummer Tilman , O'brien Philippa M. , Daly Roger J. 
Published: August 2015

DUSPs (dual-specificity phosphatases) are a heterogeneous group of protein phosphatases that can dephosphorylate both phosphotyrosine and phosphoserine/phosphothreonine residues within the one substrate. DUSPs have been implicated as major modulators of critical signalling pathways that are dysregulated in various diseases. DUSPs can be divided into six subgroups on the basis of sequence similarity that include slingshots, PRLs (phosphatases of regenerating liver), Cdc14 phosphatases (Cdc is cell division cycle), PTENs (phosphatase and tensin homologues deleted on chromosome 10), myotubularins, MKPs (mitogen-activated protein kinase phosphatases) and atypical DUSPs. Of these subgroups, a great deal of research has focused on the characterization of the MKPs. As their name suggests, MKPs dephosphorylate MAPK (mitogen-activated protein kinase) proteins ERK (extracellular-signal-regulated kinase), JNK (c-Jun N-terminal kinase) and p38 with specificity distinct from that of individual MKP proteins. Atypical DUSPs are mostly of low-molecular-mass and lack the N-terminal CH2 (Cdc25 homology 2) domain common to MKPs. The discovery of most atypical DUSPs has occurred in the last 6 years, which has initiated a large amount of interest in their role and regulation. In the past, atypical DUSPs have generally been grouped together with the MKPs and characterized for their role in MAPK signalling cascades. Indeed, some have been shown to dephosphorylate MAPKs. The current literature hints at the potential of the atypical DUSPs as important signalling regulators, but is crowded with conflicting reports. The present review provides an overview of the DUSP family before focusing on atypical DUSPs, emerging as a group of proteins with vastly diverse substrate specificity and function.
Molecular characterization of gp40, a mucin-type glycoprotein from the apical plasma membrane of Madin–Darby canine kidney cells (type I)
Authors: ZIMMER Gert , LOTTSPEICH Friedrich , MAISNER Andrea , KLENK Hans-Dieter , HERRLER Georg 
Published: August 2015

gp40 has been recently identified as a major apical cell-surface sialoglycoprotein of type-I Madin–Darby canine kidney cells, a cell line widely used for the study of polarized transport. The determination of two internal amino acid sequences of the purified glycoprotein by Edman degradation enabled us to isolate the cDNA encoding the 18.6 kDa protein backbone of gp40. Sequence analysis revealed that gp40 is a type-I membrane protein which has several characteristics in common with glycophorin A and other mucin-type glycoproteins. At least 14 serine/threonine residues were found to be used for O-glycosylation. No potential sites for N-glycosylation were detected. gp40 turned out to represent the canine homologue of a cell-surface antigen expressed by various epithelial and non-epithelial cells in rat and mouse. Potential O-glycosylation sites, transmembrane and cytoplasmic domains were found to be highly conserved in the three species. gp40 was detected in canine lung, intestine, kidney, brain and heart but not in liver and spleen. The subline II of Madin–Darby canine kidney cells was found not to express gp40. Stable expression of gp40 in transfected type-II cells revealed that gp40 is predominantly delivered to the apical plasma membrane. N-Glycans and a glycosylphosphatidylinositol anchor, both proposed apical targeting signals, are absent from gp40, indicating that other determinants are responsible for its polarized transport.
Tissue-specific promoters of the α human folate receptor gene yield transcripts with divergent 5′ leader sequences and different translational efficiencies
Authors: ROBERTS Susan J. , CHUNG Koong-Nah , NACHMANOFF Kirsten , ELWOOD Patrick C. 
Published: August 2015

The α human folate receptor (αhFR), or KB cell folate receptor, gene contains two major promoters that produce transcripts, KB1 and KB4, varying only in the length and sequence of their 5′ untranslated regions (UTRs). Using RNase protection assays specific for each isoform, we show that the level of expression of these two transcripts is tissue-specific, indicating that promoter usage is regulated, not constitutive. RNA stabilities and translational efficiencies of the KB1 and KB4 transcripts were compared to determine the functional significance of the different 5′ UTRs. Analyses of RNA turnover in vivo with actinomycin D to block new transcription and in vitro with a cytoplasmic extract indicate no discernible differences in the stabilities of the two transcripts. However, the KB4 transcript is 2–3-fold more efficiently translated in wheat germ extracts in vitro and transfected CHO cells in vivo. Also, high ionic strength, which favours the formation of RNA secondary structure, differentially affects the translational efficiencies of the two transcripts. Translation of the longer KB1 mRNA is 2–5-fold more inhibited by hypertonic conditions than translation of the KB4 mRNA. Because the 5′ UTR of KB1 is approximately four times longer than the 5′ UTR of KB4, 149 bp (75%) of the KB1 5′ UTR were deleted to determine whether the long leader sequence inhibited translation. The resulting derivative, dKB1, has a 5′ UTR similar in length, but not sequence, to the 5′ UTR of KB4. dKB1 is translated at a level approaching that of KB4 in wheat germ extracts, indicating that the upstream portion of the 5′ leader sequence contributes to the relative translational inefficiency of KB1. Hence, one consequence of tissue-specific promoter usage is the production of αhFR transcripts with different 5′ non-coding regions that affect translational efficiency.
A novel type of glutathione peroxidase: expression and regulation during wound repair
Authors: MUNZ Barbara , FRANK Stefan , HÜBNER Griseldis , OLSEN Eydfinnur , WERNER Sabine 
Published: August 2015

We have previously identified and cloned a novel keratinocyte growth factor (KGF)-regulated gene in human keratinocytes that encodes the human homologue of a bovine non-selenium glutathione peroxidase (GPx). To gain insight into the regulation of this gene in vivo, we isolated the murine homologue from a mouse skin cDNA library. In vitro transcription/translation demonstrated that the cDNA encodes a 27 kDa protein. Furthermore, we amplified by PCR a partial cDNA that most likely corresponds to a related gene. RNase protection analysis revealed tissue-specific expression of both genes and the occurrence of alternative splicing or RNA editing of at least one of the primary transcripts. Similar to that of KGF, expression of GPx was strongly induced after cutaneous injury, and each isoform displayed unique kinetics of expression during the repair process. In situ hybridization studies demonstrated high levels of GPx mRNA in keratinocytes of the hyperproliferative epithelium at the wound edge. Since these cells express functional KGF receptors, induction of GPx expression by KGF might also occur in vivo. These data suggest a role for GPx in the protection of epithelial cells against oxidative stress, particularly during the inflammatory phase of wound repair.
Purification and properties of DNase γ from apoptotic rat thymocytes
Authors: SHIOKAWA Daisuke , OHYAMA Harumi , YAMADA Takeshi , TANUMA Sei-ichi 
Published: August 2015

We previously identified three distinct DNA endonucleases, DNases α, β and γ, present in rat thymocyte nuclei. On the basis of their enzymic and biochemical properties, γ-type DNase was regarded as a candidate for the apoptotic endonuclease. Here we purified DNase γ to apparent homogeneity from apoptotic rat thymocyte nuclei induced by X-irradiation and characterized its properties in detail. The purified DNase γ exhibited one predominant protein band on SDS/PAGE and an endonuclease activity in a zymography with an estimated molecular mass of 33 kDa. The molecular mass of the native form determined by G2000SW gel-filtration HPLC was 30 kDa. Amino acid analysis showed that the amino acid composition of DNase γ was similar to that of rat DNase I (molecular mass 32 kDa) but different with regard to alanine and lysine residues. The N-terminal amino acid sequence of DNase γ was revealed to be not identical with that of rat DNase I. In accordance with previous studies, homogeneously purified DNase γ requires both Ca2+ and Mg2+ for activity. This requirement could be partially supplied by Mn2+. Of the bivalent metal ions tested, Co2+, Ni2+, Cu2+ and Zn2+ inhibited DNase γ activity. These bivalent cations also suppressed apoptotic DNA fragmentation in rat thymocytes irradiated by X-rays. The same order of inhibitory ability was observed for these bivalent metal ions in vivo(in intact cells) and in vitro, suggesting that the suppression of apoptotic DNA fragmentation at the cellular level is due to the inhibition of DNase γ. DNase γ activity was found to exist at high levels in spleen, lymph node, thymus, liver and kidney, but little was present in brain, heart or pancreas. On the basis of these findings, together with previous data, we conclude that DNase γ is a novel DNase I-like endonuclease responsible for internucleosomal cleavage of chromatin during thymic apoptosis.