bluuebunny/crossref_metadata_2025_split huggingface dataset:
Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network
Authors: Heavner Benjamin D , Smallbone Kieran , Barker Brandon , Mendes Pedro , Walker Larry P 
Published: June 2012

Abstract

Background
Efforts to improve the computational reconstruction of the Saccharomyces cerevisiae biochemical reaction network and to refine the stoichiometrically constrained metabolic models that can be derived from such a reconstruction have continued since the first stoichiometrically constrained yeast genome scale metabolic model was published in 2003. Continuing this ongoing process, we have constructed an update to the Yeast Consensus Reconstruction, Yeast 5. The Yeast Consensus Reconstruction is a product of efforts to forge a community-based reconstruction emphasizing standards compliance and biochemical accuracy via evidence-based selection of reactions. It draws upon models published by a variety of independent research groups as well as information obtained from biochemical databases and primary literature.

Results
Yeast 5 refines the biochemical reactions included in the reconstruction, particularly reactions involved in sphingolipid metabolism; updates gene-reaction annotations; and emphasizes the distinction between reconstruction and stoichiometrically constrained model. Although it was not a primary goal, this update also improves the accuracy of model prediction of viability and auxotrophy phenotypes and increases the number of epistatic interactions. This update maintains an emphasis on standards compliance, unambiguous metabolite naming, and computer-readable annotations available through a structured document format. Additionally, we have developed MATLAB scripts to evaluate the model’s predictive accuracy and to demonstrate basic model applications such as simulating aerobic and anaerobic growth. These scripts, which provide an independent tool for evaluating the performance of various stoichiometrically constrained yeast metabolic models using flux balance analysis, are included as Additional files 1, 2 and 3.

Conclusions
Yeast 5 expands and refines the computational reconstruction of yeast metabolism and improves the predictive accuracy of a stoichiometrically constrained yeast metabolic model. It differs from previous reconstructions and models by emphasizing the distinction between the yeast metabolic reconstruction and the stoichiometrically constrained model, and makes both available as Additional file 4 and Additional file 5 and at http://yeast.sf.net/ as separate systems biology markup language (SBML) files. Through this separation, we intend to make the modeling process more accessible, explicit, transparent, and reproducible.
Giant cell tumor of the distal ulna: a case report
Authors: Vanni Daniele , Pantalone Andrea , Andreoli Elda , Caldora Patrizio , Salini Vincenzo 
Published: June 2012

AbstractIntroductionSeveral cases of long bone giant cell tumor have been reported in the literature. We report the case of a patient with a giant cell tumor in the distal ulna. This is very unusual, with a reported incidence of 0.45 to 6%.Case presentationA 17-year-old Colombian man presented with a painful swelling of the left wrist. After performing an instrumental examination, a diagnosis of distal ulna giant cell tumor was made. The tumor was treated with an intralesional curettage, phenol application and bone grafting.ConclusionsThis tumor may have a good prognosis if it is diagnosed early and radically treated. It is important to be aware of atypical cancer localizations in order to perform a proper diagnosis.
Upregulation of tumor necrosis factor receptor-associated factor 6 correlated with synovitis severity in rheumatoid arthritis
Authors: Zhu Lang-Jing , Dai Lie , Zheng Dong-Hui , Mo Ying-Qian , Ou-Yang Xia , Wei Xiu-Ning , Shen Jun , Zhang Bai-Yu 
Published: June 2012

Abstract

Introduction

Rheumatoid arthritis (RA) is a chronic inflammatory disease leading to joint destruction and disability. Focal bone erosion is due to excess bone resorption of osteoclasts. Tumor necrosis factor receptor-associated factor 6 (TRAF6) is one of the critical mediators both in inflammatory signal pathway and differentiation and resorption activity of osteoclasts. Here we aimed to investigate TRAF6 expression in RA synovium and its correlation with histological synovitis severity and radiological joint destruction in RA.

Methods

Synovitis score was determined in needle biopsied synovium from 44 patients with active RA. Synovium from nine patients with osteoarthritis (OA) and seven with orthopedic arthropathies (Orth.A) were enrolled as "less inflamed" disease controls. Serial sections were stained immunohistochemically for TRAF6 as well as CD68 (macrophage), CD3 (T cell), CD20 (B cell), CD38 (plasmocyte), CD79a (B lineage cells from pre-B cell to plasmocyte stage), and CD34 (endothelial cell). Double immunofluorescence staining of TRAF6 and CD68 were tested. Densities of positive staining cells were determined and correlated with histological disease activity (synovitis score) and radiographic joint destruction (Sharp score).

Results

TRAF6 expression was found in the intimal and subintimal area of RA synovium, with intense staining found in the endochylema and nucleus of intimal synoviocytes and subintimal inflammatory cells. Double immunofluorescence staining showed TRAF6 was expressed in most of the intimal cells and obviously expressed in CD68+ cells and some other CD68- cells in subintimal area. Synovial TRAF6 was significantly over-expressed in the RA group compared with the OA and Orth.A group (2.53 ± 0.94 vs. 0.72 ± 0.44 and 0.71 ± 0.49, P < 0.0001). Synovial TRAF6 expression in RA correlated significantly with synovitis score (r = 0.412, P = 0.006), as well as the inflammatory cell infiltration (r = 0.367, P = 0.014). Significant correlation was detected between synovial TRAF6 expression and intimal CD68+ cells, as well as the cell density of subintimal CD68+ cells, CD3+ cells, CD20+ cells, CD38+ cells, and CD79a+ cells (all P < 0.05).

Conclusions

Elevated synovial TRAF6 expression correlated with synovitis severity and CD68+ cell density in RA. It is, therefore, hypothesized that synovial TRAF6 is involved in the pathogenesis of synovial inflammation and osteoclast differentiation in RA.
Ex vivo imaging of mouse brain using micro-CT with non-ionic iodinated contrast agent: a comparison with myelin staining
Authors: Saito S , Murase K 
Published: June 2012

Objective
We investigated the use of micro-CT with contrast agent for the non-invasive characterisation of fixed mouse brain tissue specimens as a means to differentiate between grey and white matter.

Methods
Nine mice were divided into two groups for micro-CT (n=6) and myelin staining (n=3) experiments. Six mice underwent in vivo micro-CT and were then prepared for brain specimens by transcardiac perfusion with paraformaldehyde. The six mouse brains were soaked in two different concentrations of non-ionic iodinated contrast agents (60 and 150 mg ml−1). Immersion times used for each concentration of iodine were for 3, 7 and 14 days. Three-dimensional ex vivo micro-CT images were acquired with a resolution of 39 μm3 to create isotropic images. The other three mice were stained for evaluation of the myelin structure.

Results
Soaking the brains in non-ionic iodinated contrast agent resulted in clear differences in signal between the grey matter, the white matter and the ventricular spaces. The 150 mg ml−1 contrast agent solution yielded images with better contrast-to-noise ratio (CNR) than 60 mg ml−1 iodine contrast agent solution. 14 days of soaking yielded images with better CNR than 3 and 7 days. The CT contrast of grey and white matter derived from the iodine-soaked fixed brains was strongly related to tissue myelin.

Conclusion
The present study demonstrated that micro-CT can be used to detect the mouse brain myelin structure at 3, 7 and 14 days after fixation using a CT contrast agent.
Totally implantable venous power ports of the forearm and the chest: initial clinical experience with port devices approved for high-pressure injections
Authors: Goltz J P , Noack C , Petritsch B , Kirchner J , Hahn D , Kickuth R 
Published: June 2012

Objectives
To evaluate the technical success, clinical outcome and safety of percutaneously placed totally implantable venous power ports (TIVPPs) approved for high-pressure injections, and to analyse their value for arterial phase CT scans.

Methods
Retrospectively, we identified 204 patients who underwent TIVPP implantation in the forearm (n=152) or chest (n=52) between November 2009 and May 2011. Implantation via an upper arm (forearm port, FP) or subclavian vein (chest port, CP) was performed under sonographic and fluoroscopic guidance. Complications were evaluated following the standards of the Society of Interventional Radiology. Power injections via TIVPPs were analysed, focusing on adequate functioning and catheter's tip location after injection. Feasibility of automatic bolus triggering, peak injection pressure and arterial phase aortic enhancement were evaluated and compared with 50 patients who had had power injections via classic peripheral cannulas.

Results
Technical success was 100%. Procedure-related complications were not observed. Catheter-related thrombosis was diagnosed in 15 of 152 FPs (9.9%, 0.02/100 catheter days) and in 1 of 52 CPs (1.9%, 0.002/100 catheter days) (p&lt;0.05). Infectious complications were diagnosed in 9 of 152 FPs (5.9%, 0.014/100 catheter days) and in 2 of 52 CPs (3.8%, 0.003/100 catheter days) (p&gt;0.05). Arterial bolus triggering succeeded in all attempts; the mean injection pressure was 213.8 psi. Aortic enhancement did not significantly differ between injections via cannulas and TIVPPs (p&gt;0.05).

Conclusions
TIVPPs can be implanted with high technical success rates, and are associated with low rates of complications if implanted with sonographic and fluoroscopic guidance. Power injections via TIVPPs are safe and result in satisfying arterial contrast. Conventional ports should be replaced by TIVPPs.
Circulating Human Hepcidin-25 Concentrations Display a Diurnal Rhythm, Increase with Prolonged Fasting, and Are Reduced by Growth Hormone Administration
Authors: Troutt Jason S , Rudling Mats , Persson Lena , Ståhle Lars , Angelin Bo , Butterfield Anthony M , Schade Andrew E , Cao Guoqing , Konrad Robert J 
Published: June 2012

Abstract

BACKGROUND
Hepcidin-25 reduces iron absorption by binding to the intestinal iron transporter ferroportin and causing its degradation. Currently, little is known about the basal regulation of circulating hepcidin-25. In addition, although erythropoietin administration has been reported to decrease the circulating hepcidin concentration, information is limited regarding how other stimulators of erythropoiesis, such as growth hormone (GH), might alter hepcidin-25 concentrations.

METHODS
We used a sensitive and specific hepcidin-25 dual–monoclonal antibody sandwich immunoassay to measure hepcidin-25 in healthy human volunteers at various time points throughout the day and during 3 days of fasting and subsequent refeeding. We also measured hepcidin-25 concentrations in healthy volunteers after GH administration.

RESULTS
In healthy individuals, hepcidin-25 concentrations displayed a diurnal variation, with concentrations being lowest in the early morning and steadily increasing throughout the day before declining during the evening hours, a pattern that was not influenced by food intake. Prolonged fasting produced statistically significant increases in hepcidin-25 concentrations. Refeeding reversed this process, and GH administration markedly decreased hepcidin-25 concentrations.

CONCLUSIONS
Our results indicate that in humans, hepcidin-25 exhibits diurnal changes that can be altered by prolonged fasting, which increases hepcidin-25 concentrations approximately 3-fold after 3 days of fasting, possibly owing to a suppression of erythropoiesis that may occur during the fasting state to preserve tissue iron concentrations. In contrast, GH administration decreased hepcidin-25 concentrations by approximately 65%, presumably by stimulating erythropoiesis. These results indicate that circulating hepcidin-25 concentrations display much more dynamic and rapid variation than might have been anticipated previously.
Party Systems, Critical Junctures, and Cleavages in Southeast Asia
Authors: Ufen Andreas 
Published: June 2012

Abstract
This article differentiates between clientelist (Thailand and the Philippines) and cleavage-based parties and party systems (Malaysia and Indonesia) with reference to insights of historical institutionalism. Clientelist parties, in contrast to cleavage-based ones, often undermine democratization because, on average, representativeness is weak, bureaucracy is more politicized, and rent-seeking behavior is widespread.
Polymorphisms of the drug transporter gene ABCB1 predict side effects of treatment with cabergoline in patients with PRL adenomas
Authors: Athanasoulia A P , Sievers C , Ising M , Brockhaus A C , Yassouridis A , Stalla G K , Uhr M 
Published: June 2012

IntroductionTreatment with dopamine agonists in patients with prolactin (PRL) adenomas and Parkinson's disease is associated with central side effects. Central side effects may depend on a substance's ability to pass the blood–brain barrier, which can be actively controlled by transporter molecules such as the P-glycoprotein (P-gp) encoded by theABCB1gene.Materials and methodsWe aimed to determine whether cabergoline is transported by the P-gp and whether polymorphisms of its encodingABCB1gene predict central side effects of cabergoline therapy in patients with PRL adenomas. i) In an experimental mouse model lacking the homologues of the humanABCB1gene (Abcb1abdouble knockout mouse model), we examined whether cabergoline is a substrate of the P-gp using eight mutant and eight wild-type mice. ii) In a human case–control study including 79 patients with PRL adenomas treated with cabergoline at the Max Planck Institute of Psychiatry in Munich, we investigated the association of four selectedABCB1gene single nucleotide polymorphisms (SNPs) (rs1045642, rs2032582, rs2032583 and rs2235015), with the occurrence of central side effects under cabergoline therapy.Resultsi) In the experimental mouse model, we observed that brain concentrations of cabergoline were tenfold higher in the mutant mice compared with their wild-type littermates, implying that cabergoline is indeed a substrate of the transporter P-gp at the blood–brain barrier level. ii) In the human study, we observed significant negative associations under cabergoline for the C-carriers and heterozygous CT individuals of SNP rs1045642 with two central side effects (frequency of fatigue and sleep disorders) and for the G-carriers of SNP rs2032582 with the enhancement of dizziness. For the SNPs rs2235015 and rs2032583, no associations with central side effects under cabergoline were found.DiscussionThis is the first study demonstrating that individualABCB1gene polymorphisms, reflecting a different expression and function of the P-gp, could predict the occurrence of central side effects under cabergoline. Our findings can be viewed as a step into personalised therapy in PRL adenoma patients.
Genome Rearrangements Caused by Depletion of Essential DNA Replication Proteins inSaccharomyces cerevisiae
Authors: Cheng Edith , Vaisica Jessica A , Ou Jiongwen , Baryshnikova Anastasia , Lu Yong , Roth Frederick P , Brown Grant W 
Published: June 2012

AbstractGenetic screens of the collection of ∼4500 deletion mutants in Saccharomyces cerevisiae have identified the cohort of nonessential genes that promote maintenance of genome integrity. Here we probe the role of essential genes needed for genome stability. To this end, we screened 217 tetracycline-regulated promoter alleles of essential genes and identified 47 genes whose depletion results in spontaneous DNA damage. We further showed that 92 of these 217 essential genes have a role in suppressing chromosome rearrangements. We identified a core set of 15 genes involved in DNA replication that are critical in preventing both spontaneous DNA damage and genome rearrangements. Mapping, classification, and analysis of rearrangement breakpoints indicated that yeast fragile sites, Ty retrotransposons, tRNA genes, early origins of replication, and replication termination sites are common features at breakpoints when essential replication genes that suppress chromosome rearrangements are downregulated. We propose mechanisms by which depletion of essential replication proteins can lead to double-stranded DNA breaks near these features, which are subsequently repaired by homologous recombination at repeated elements.
On the Prospects of Whole-Genome Association Mapping inSaccharomyces cerevisiae
Authors: Connelly Caitlin F , Akey Joshua M 
Published: June 2012

AbstractAdvances in sequencing technology have enabled whole-genome sequences to be obtained from multiple individuals within species, particularly in model organisms with compact genomes. For example, 36 genome sequences of Saccharomyces cerevisiae are now publicly available, and SNP data are available for even larger collections of strains. One potential use of these resources is mapping the genetic basis of phenotypic variation through genome-wide association (GWA) studies, with the benefit that associated variants can be studied experimentally with greater ease than in outbred populations such as humans. Here, we evaluate the prospects of GWA studies in S. cerevisiae strains through extensive simulations and a GWA study of mitochondrial copy number. We demonstrate that the complex and heterogeneous patterns of population structure present in yeast populations can lead to a high type I error rate in GWA studies of quantitative traits, and that methods typically used to control for population stratification do not provide adequate control of the type I error rate. Moreover, we show that while GWA studies of quantitative traits in S. cerevisiae may be difficult depending on the particular set of strains studied, association studies to map cis-acting quantitative trait loci (QTL) and Mendelian phenotypes are more feasible. We also discuss sampling strategies that could enable GWA studies in yeast and illustrate the utility of this approach in Saccharomyces paradoxus. Thus, our results provide important practical insights into the design and interpretation of GWA studies in yeast, and other model organisms that possess complex patterns of population structure.
BRCAness: Finding the Achilles Heel in Ovarian Cancer
Authors: Rigakos Georgios , Razis Evangelia 
Published: June 2012

Abstract
Ovarian cancer is the leading cause of death among gynecological cancers. It exhibits great heterogeneity in tumor biology and treatment response. Germline mutations of DNA repair genes BRCA1/2 are the fundamental defects in hereditary ovarian cancer that expresses a distinct phenotype of high response rates to platinum agents, improved disease-free intervals and survival rates, and high-grade serous histology. The term “BRCAness” describes the phenotypic traits that some sporadic ovarian tumors share with tumors in BRCA1/2 germline mutation carriers and reflects similar causative molecular abnormalities. BRCA pathway studies and molecular profiling reveal BRCA-related defects in almost half of the cases of ovarian cancer. BRCA-like tumors are particularly sensitive to DNA-damaging agents (e.g., platinum agents) because of inadequate BRCA-mediated DNA repair mechanisms, such as nucleotide-excision repair and homologous recombination (HR). Additional inhibition of other DNA repair pathways leads to synthetic lethality in HR-deficient cells; this has been employed in the treatment of BRCA-like ovarian tumors with poly(ADP-ribose) polymerase inhibitors with promising results. This article presents a comprehensive review of the relevant literature on the role of BRCAness in ovarian cancer with respect to BRCA function, methods of BRCA epigenetic defect detection and molecular profiling, and the implications of BRCA dysfunction in the treatment of ovarian cancer.
Manipulating the intrinsic parameters of propagule pressure: implications for bio‐invasion
Authors: Hedge Luke H. , O'Connor Wayne A. , Johnston Emma L. 
Published: June 2012

Much effort has been devoted to understanding the factors promoting species colonisation, and processes that may cause small incipient populations to fail. Post colonisation and community level processes are proving to be less reliable predictors of initial population size and propagule pressure is now posited as a key predictor of species establishment. Yet, empirical studies manipulating the intrinsic parameters of propagule pressure, such as arrival frequency (number), and intensity (size) are lacking. Understanding colonisation and incipient population survival is particularly important in the field of bio‐invasions. Propagule pressure is now often cited as a key determinant of invasion success, yet we have few empirical tests manipulating the intrinsic parameters of propagule pressure. We conducted a series of factorial field experiments utilizing larvae of the cosmopolitan invasive oyster Crassostrea gigas. A newly developed technique was used to quantitatively alter the size of propagules and the frequency at which they arrive. When total propagule pressure was held constant, and the size and arrival frequency was altered, frequent small inoculations dramatically increased incipient population size >65% relative to infrequent large introductions. We also found that smaller, less dense inoculations resulted in >85% greater proportional settlement and colonisation of this cosmopolitan species. Predation altered the overall survival of incipient oyster populations, but did not alter this pattern.Our findings may help explain patterns of ballast water and hull‐fouling introductions, as ports and harbours that receive frequent exposure to invasive propagules from the same source location will be at greater risk of invasion.
Reliability of a Treatment-Based Classification System for Subgrouping People With Low Back Pain
Authors: Henry Sharon M. , Fritz Julie M. , Trombley Andrea R. , Bunn Janice Y. 
Published: June 2012

Study Design Observational, cross-sectional reliability study. Objectives To examine the interrater reliability of novice raters in their use of the treatment-based classification (TBC) system for low back pain and to explore the patterns of disagreement in classification errors. Background Although the interrater reliability of individual test items in the TBC system is moderate to good, some error persists in classification decision making. Understanding which classification errors are common could direct further refinement of the TBC system. Methods Using previously recorded patient data (n = 24), 12 novice raters classified patients according to the TBC schema. These classification results were combined with those of 7 other raters, allowing examination of the overall agreement using the kappa statistic, as well as agreement/disagreement among pairwise comparisons in classification assignments. A chi-square test examined differences in percent agreement between the novice and more experienced raters and differences in classification distributions between these 2 groups of raters. Results Among 12 novice raters, there was 80.9% agreement in the pairs of classification (κ = 0.62; 95% confidence interval: 0.59, 0.65) and an overall 75.5% agreement (κ = 0.57; 95% confidence interval: 0.55, 0.69) for the combined data set. Raters were least likely to agree on a classification of stabilization (77.5% agreement). The overall percentage of pairwise classification judgments that disagreed was 24.5%, with the most common disagreement being between manipulation and stabilization (11.0%), followed by a mismatch between stabilization and specific exercise (8.2%). Conclusion Additional refinement is needed to reduce rater disagreement that persists in the TBC decision-making algorithm, particularly in the stabilization category. J Orthop Sports Phys Ther 2012;42(9):797–805, Epub 7 June 2012. doi:10.2519/jospt.2012.4078