bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rank-based genome-wide analysis reveals the association of Ryanodine receptor-2 gene variants with childhood asthma among human populations
Authors: Ding Lili , Abebe Tilahun , Beyene Joseph , Wilke Russell A , Goldberg Arnon , Woo Jessica G , Martin Lisa J , Rothenberg Marc E , Rao Marepalli , Hershey Gurjit K Khurana , Chakraborty Ranajit , Mersha Tesfaye B 
Published: July 2013

Abstract

Background
The standard approach to determine unique or shared genetic factors across populations is to identify risk alleles in one population and investigate replication in others. However, since populations differ in DNA sequence information, allele frequencies, effect sizes, and linkage disequilibrium patterns, SNP association using a uniform stringent threshold on p values may not be reproducible across populations. Here, we developed rank-based methods to investigate shared or population-specific loci and pathways for childhood asthma across individuals of diverse ancestry. We performed genome-wide association studies on 859,790 SNPs genotyped in 527 affected offspring trios of European, African, and Hispanic ancestry using publically available asthma database in the Genotypes and Phenotypes database.

Results
Rank-based analyses showed that there are shared genetic factors for asthma across populations, more at the gene and pathway levels than at the SNP level. Although the top 1,000 SNPs were not shared, 11 genes (RYR2, PDE4D, CSMD1, CDH13, ROBO2, RBFOX1, PTPRD, NPAS3, PDE1C, SEMA5A, and CTNNA2) mapped by these SNPs were shared across populations. Ryanodine receptor 2 (RYR2, a statin response-related gene) showed the strongest association in European (p value = 2.55 × 10−7) and was replicated in African (2.57 × 10−4) and Hispanic (1.18 × 10−3) Americans. Imputation analyses based on the 1000 Genomes Project uncovered additional RYR2 variants associated with asthma. Network and functional ontology analyses revealed that RYR2 is an integral part of dermatological or allergic disorder biological networks, specifically in the functional classes involving inflammatory, eosinophilic, and respiratory diseases.

Conclusion
Our rank-based genome-wide analysis revealed for the first time an association of RYR2 variants with asthma and replicated previously discovered PDE4D asthma gene across human populations. The replication of top-ranked asthma genes across populations suggests that such loci are less likely to be false positives and could indicate true associations. Variants that are associated with asthma across populations could be used to identify individuals who are at high risk for asthma regardless of genetic ancestry.
Characterization of sample preparation methods of NIH/3T3 fibroblasts for ToF-SIMS analysis
Authors: Robinson Michael A , Castner David G 
Published: July 2013

The information that is obtained from single cells during time-of-flight secondary ion mass spectrometry (ToF-SIMS) analysis is influenced by the method that was used to prepare the cells. The removal of extracellular media before analysis is necessary, but the rinsing technique should not damage the plasma membrane of the cell. The presence of intracellular salts reduced the secondary ion yield an average of 2.6-fold during Bi3+/C60++ depth profiles. Chemical fixation followed by rinsing removed a majority of the intracellular salts, “recovering” the positive secondary ion yields. The formaldehyde-fixation process removed a majority of the intracellular Cl-, but other key anions were not removed in significant amounts. The data presented here is consistent the anion neutralization mechanism largely responsible for the lower ion yields. All of the organic secondary ions that were detected in the freeze-dried cells were also detected in the formaldehyde-fixed cells, suggesting that the fixation process did not remove any molecular species to an extent that is detectable by ToF-SIMS. Compared to freeze dried cells, well preserved, frozen-hydrated cells showed little increase, or a decreased yield, for most low mass ions, but an increased yield for larger mass fragments. This is consistent with a reduced damage cross section at cryogenic analysis temperatures, although proton donation from water and reduction the salt effects in the presence of water likely also play roles. Numerous ions detected from the frozen-hydrated cells were not detected from the freeze dried cells, however many of these ions were attributed to chemical combinations of water, salts and the ammonium acetate rinsing solution.

Supplementary Material
Additional file 1: Figure S1: (A) Na+ peak and (B) 41 K+ peak from the depth profile of FH cells. The K+/Na+ ratio is 14.7, signifying the cells were well preserved. The 41 K+ isotope peak was used due to detector saturation of the 39 K+ isotope peak. [13758_2013_15_MOESM1_ESM.pdf (42 KB)]
Additional file 2: Figure S2: (A) Depth profile from cells that were freeze-dried. (B) Depth profile from cells that were chemically fixed with formaldehyde. (C) Depth profile from cells that were analyzed frozen-hydrated. The depth profiles were normalized by the Bi3 + ion dose. [13758_2013_15_MOESM2_ESM.pdf (311 KB)]
Additional file 3: Table S1: All positive secondary ions detected from both the FD and FF cells. Sorted by fold difference value, smallest to largest. [13758_2013_15_MOESM3_ESM.pdf (124 KB)]
Additional file 4: Table S2: Positive Ions that were detected from the frozen-hydrated cells but not the freeze-dried cells, or in new very low amounts in the FD cells. [13758_2013_15_MOESM4_ESM.pdf (29 KB)]
Additional file 5: Table S3: All positive secondary ions detected from both the FH cells and the FD cells. [13758_2013_15_MOESM5_ESM.pdf (52 KB)]
The systems biology simulation core algorithm
Authors: Keller Roland , Dörr Alexander , Tabira Akito , Funahashi Akira , Ziller Michael J , Adams Richard , Rodriguez Nicolas , Novère Nicolas Le , Hiroi Noriko , Planatscher Hannes , Zell Andreas , Dräger Andreas 
Published: July 2013

Abstract

Background
With the increasing availability of high dimensional time course data for metabolites, genes, and fluxes, the mathematical description of dynamical systems has become an essential aspect of research in systems biology. Models are often encoded in formats such as SBML, whose structure is very complex and difficult to evaluate due to many special cases.

Results
This article describes an efficient algorithm to solve SBML models that are interpreted in terms of ordinary differential equations. We begin our consideration with a formal representation of the mathematical form of the models and explain all parts of the algorithm in detail, including several preprocessing steps. We provide a flexible reference implementation as part of the Systems Biology Simulation Core Library, a community-driven project providing a large collection of numerical solvers and a sophisticated interface hierarchy for the definition of custom differential equation systems. To demonstrate the capabilities of the new algorithm, it has been tested with the entire SBML Test Suite and all models of BioModels Database.

Conclusions
The formal description of the mathematics behind the SBML format facilitates the implementation of the algorithm within specifically tailored programs. The reference implementation can be used as a simulation backend for Java™-based programs. Source code, binaries, and documentation can be freely obtained under the terms of the LGPL version 3 from http://simulation-core.sourceforge.net. Feature requests, bug reports, contributions, or any further discussion can be directed to the mailing list simulation-core-development@lists.sourceforge.net.
Chronic AMPK activity dysregulation produces myocardial insulin resistance in the human Arg302Gln-PRKAG2 glycogen storage disease mouse model
Authors: Thorn Stephanie L , Gollob Michael H , Harper Mary-Ellen , Beanlands Rob S , deKemp Robert A , DaSilva Jean N 
Published: July 2013

Abstract

Background
The cardiac PRKAG2 mutation in the γ2-subunit of adenosine monophosphate activated kinase (AMPK) is characterized by excessive glycogen deposition, hypertrophy, frequent arrhythmias, and progressive conduction system disease. We investigated whether myocardial glucose uptake (MGU) was augmented following insulin stimulation in a mouse model of the PRKAG2 cardiac syndrome.

Methods
Myocardial and skeletal muscle glucose uptake was assessed with 2-[18F]fluoro-2-deoxyglucose positron emission tomography imaging in n = 3 transgenic wildtype (TGwt) vs n = 7 PRKAG2 mutant (TGmut) mice at baseline and 1 week later, 30 min following acute insulin. Systolic function, cardiac glycogen stores, phospho-AMPK α, and insulin-receptor expression levels were analyzed to corroborate to the in vivo findings.

Results
TGmut Patlak Ki was reduced 56% at baseline compared to TGwt (0.3 ± 0.2 vs 0.7 ± 0.1, t test p = 0.01). MGU was augmented 71% in TGwt mice following acute insulin from baseline (0.7 ± 0.1 to 1.2 ± 0.2, t test p < 0.05). No change was observed in TGmut mice. As expected for this cardiac specific transgene, skeletal muscle was unaffected at baseline with a 33% to 38% increase (standard uptake values) for both genotypes following insulin stimulation. TGmut mice had a 47% reduction in systolic function with a fourfold increase in cardiac glycogen stores correlated with a 29% reduction in phospho-AMPK α levels. There was no difference in cardiac insulin receptor expression between mouse genotypes.

Conclusions
These results demonstrate a correlation between insulin resistance and AMPK activity and provide the basis for the use of this animal model for assessing metabolic therapy in the treatment of affected PRKAG2 patients.
Effective combination of human bone marrow mesenchymal stem cells and minocycline in experimental autoimmune encephalomyelitis mice
Authors: Hou Yun , Ryu Chung Heon , Park Kwang Ywel , Kim Seong Muk , Jeong Chang Hyun , Jeun Sin-Soo 
Published: July 2013

Abstract
Introduction
Multiple sclerosis (MS) is the most common inflammatory demyelinating disorder of the central nervous system (CNS). Minocycline ameliorates the clinical severity of MS and exhibits antiinflammatory, neuroprotective activities, and good tolerance for long-term use, whereas it is toxic to the CNS. Recently, the immunomodulation and neuroprotection capabilities of human bone marrow mesenchymal stem cells (hBM-MSCs) were shown in experimental autoimmune encephalomyelitis (EAE). In this study, we evaluated whether the combination of hBM-MSCs and a low-dose minocycline could produce beneficial effects in EAE mice.

Methods
The sensitivity of hBM-MSCs to minocycline was determined by an established cell-viability assay. Minocycline-treated hBM-MSCs were also characterized with flow cytometry by using MSC surface markers and analyzed for their multiple differentiation capacities. EAE was induced in C57BL/6 mice by using immunization with MOG35-55. Immunopathology assays were used to detect the inflammatory cells, demyelination, and neuroprotection. Interferon gamma (IFN-γ)/tumor necrosis factor alpha (TNF-α) and interleukin-4 (IL-4)/interleukin-10 (IL-10), the hallmark cytokines that direct Th1 and Th2 development, were detected with enzyme-linked immunosorbent assay (ELISA). terminal dUTP nick-end labeling (TUNEL) staining was performed to elucidate the cell apoptosis in the spinal cords of EAE mice.

Results
Minocycline did not affect the viability, surface phenotypes, or differentiation capacity of hBM-MSCs, while minocycline affected the viability of astrocytes at a high dose. In vivo efficacy experiments showed that combined treatment, compared to the use of minocycline or hBM-MSCs alone, resulted in a significant reduction in clinical scores, along with attenuation of inflammation, demyelination, and neurodegeneration. Moreover, the combined treatment with hBM-MSCs and minocycline enhanced the immunomodulatory effects, which suppressed proinflammatory cytokines (IFN-γ, TNF-α) and conversely increased anti-inflammatory cytokines (IL-4, IL-10). In addition, TUNEL staining also demonstrated a significant decrease of the number of apoptotic cells in the combined treatment compared with either treatment alone.

Conclusions
The combination of hBM-MSCs and minocycline provides a novel experimental protocol to enhance the therapeutic effects in MS.
Adapting the Short Story: Fidelity and Motivation in Sarah Polley’s Away From Her
Authors: Lister Rachel 
Published: July 2013

Abstract
This article explores the challenges of adapting modern short stories, using as a case study Away From Her (2006), Sarah Polley’s cinematic adaptation of Alice Munro’s ‘The bear came over the mountain’. Drawing on Linda Hutcheon’s adaptation theory, the article asks whether some common assumptions concerning the constraints of film can be sustained in relation to adaptations of short stories. Focusing specifically on the issue of Weltian ‘mystery’ that has become associated with the form, the article considers Polley’s claims to textual fidelity and her handling of the many tensions inherent in Munro’s elliptical story. The article pays particular attention to Polley’s treatment of the story’s silences and absences and highly ambiguous ending. It considers Polley’s manipulation of dialogue and visual and aural cues and argues that she ultimately compromises the story’s mystery through the elaboration of narrative structures favoured by Hollywood: the love story and the discovery story.
Reviews
Authors: Poore Dr Benjamin , Raw Laurence 
Published: July 2013

Abstract
In/Fidelity: Essays on Film Adaptation, David L. Kranz and Nancy C. Mellerski (eds) (2008) Newcastle: Cambridge Scholars Publishing, 251 pp., ISBN: 9781847184023, h/bk, £34.99
The Radio Drama Handbook, Richard J. Hand and Mary Traynor (2011) London and New York: Continuum, 227 pp., ISBN: 978-1-4411-4743-1, p/bk, £14.95.
Can Horizontal Mergers Without Synergies Increase Consumer Welfare? Cournot and Bertrand Competition Under Uncertain Demand
Authors: Shieh Shiou , Huang Chi-Fei , Chen Hsiao-Chi 
Published: July 2013

Abstract
We analyze the welfare effects of horizontal mergers in a model wherein firms produce differentiated products and possess asymmetric information about uncertain market demand. Mergers do not bring about synergies or cost savings, but do allow firms to share their market demand information. We find that under Cournot competition, mergers without synergies could increase expected consumer surplus and social welfare, provided that market volatility is sufficiently large. The parameter spaces in which mergers are beneficial to consumers and society widen when products are more differentiated. In contrast, under Bertrand competition, mergers are always welfare reducing regardless of the degree of market volatility and extent of product differentiation. The driving force for the contrasting results lies in opposing welfare effects of information sharing in the contexts of quantity and price setting.
A hybrid Euler–Hadamard product and moments of ζ'(ρ)
Authors: Bui H. M. , Gonek S. M. , Milinovich M. B. 
Published: July 2013

Abstract
Keating and Snaith modeled the Riemann zeta-function ζ(s) by characteristic polynomials of random N×N unitary matrices, and used this to conjecture the asymptotic main term for the 2k-th moment of ζ(1/2+i
t) when
k > -1/2. However, an arithmetical factor, widely believed to be part of the leading term coefficient, had to be inserted in an ad hoc manner. Gonek, Hughes and Keating later developed a hybrid formula for ζ(s) that combines a truncation of its Euler product with a product over its zeros. Using it, they recovered the moment conjecture of Keating and Snaith in a way that naturally includes the arithmetical factor. Here we use the hybrid formula to recover a conjecture of Hughes, Keating and O'Connell concerning the discrete moments of the derivative of the Riemann zeta-function averaged over the zeros of ζ(s), incorporating the arithmetical factor in a natural way.
Purification of Crude Glycerine Obtained from Transesterification of Cottonseed Oil
Authors: Ferreira Marcionila O. , M.B.D. Sousa Elisa , Pereira Camila G. 
Published: July 2013

Abstract
The objective of this study was to purify glycerine obtained from the transesterification of cottonseed oil, using ion exchange resins. The batch process used strong cation, weak anion and a mixture of its resins. The purified glycerine was characterized as to metal content, colour and glycerol content. The experiments were conducted using the resins individually and in series. In the experiments in series, there was a constant decrease in conductivity. Analyses without the use of charcoal showed that conductivity behaved similarly to that of treatment with charcoal. For conductivity tests using activated charcoal and individual resins, the mixed resin produced the best result when compared to commercial glycerine.Considering the analysis made with activated carbon, when the glycerine solution was treated with individual resins, it was observed that the conditions established for treatment with 10 g of resin, 5 hours of contact with each resin and 50 mL of glycerine, its conductivity decreased to the cation exchange resin, increased to anionic resin and had a variable value with respect to the mixed resin. In serial processing, there was a steady decrease in the conductivity of the glycerine solution. The content of glycerol, after the solution had been passed through activated charcoal, 56% of the compound was recovered. It was also observed that the mixed resin retained a lower amount of glycerol. It can be concluded that ion exchange resins were efficient in treating the glycerine solution in all the tests, since there was little glycerol retention and high undesirable compound retention.
Crystal structure of catena-poly[aqua-µ-1,4-benzenedicarboxylato-κ2O:O'-3,5-dimethyl-4-phenyl-1,2,4-triazole-κN-zinc(II)] monohydrate, Zn(H2O)(C8H4O4)(C10H11N3)·H2O, C18H17N3O6Zn
Authors: Chen Ming-Ming , Chen Shui-Sheng , Sheng Liang-Quan 
Published: July 2013

Abstract C18H17N3O6Zn, triclinic, P1̅ (no. 2), a = 10.0780(5) Å, b = 10.1678(5) Å, c = 10.3591(5) Å, α = 83.119(1)°, β = 81.178(2)°, γ = 64.753(1)°, V = 947.0 Å3, Z = 2, Rgt(F) = 0.0285, wRref(F2) = 0.1213, T = 296 K.
Crystal structure of bis-5-(pyridin-2-yl)pyrazine-2-carboxylic acid silver( I) triflate – acetonitrile (1:2), [Ag(C10H7N3O2)2](CF3SO3)·2CH3CN, C24H20AgF3N8O7S2
Authors: Li Jing , Zhang Zhan Min , Ma Jun , Liu Feng Juan , Zhou Lei 
Published: July 2013

Abstract C24H20AgF3N8O7S2, monoclinic, C2/c (no. 15), a = 31.864(5) Å, b = 6.7191(10) Å, c = 14.052(2) Å, β = 97.006(3)°, V = 2986.0 Å3, Z = 4, Rgt(F) = 0.0606, wRref(F2) = 0.1637, T = 293 K.
MARS therapy, the bridging to liver retransplantation — Three cases from the Hungarian liver transplant program
Authors: Pőcze Balázs , Fazakas János , Zádori Gergely , Görög Dénes , Kóbori László , Dabasi Eszter , Mándli Tamás , Piros László , Smudla Anikó , Szabó Tamás , Toronyi Éva , Tóth Szabolcs , Tőzsér Gellért , Végső Gyula , Doros Attila , Nemes Balázs 
Published: July 2013

AbstractBesides orthotopic liver transplantation (OLT) there is no long-term and effective replacement therapy for severe liver failure. Artificial extracorporeal liver supply devices are able to reduce blood toxin levels, but do not replace any synthetic function of the liver. Molecular adsorbent recirculating system (MARS) is one of the methods that can be used to treat fulminant acute liver failure (ALF) or acute on chronic liver failure (AoCLF). The primary non-function (PNF) of the newly transplanted liver manifests in the clinical settings exactly like acute liver failure. MARS treatment can reduce the severity of complications by eliminating blood toxins, so that it can help hepatic encephalopathy (HE), hepatorenal syndrome (HRS), and the high rate mortality of cerebral herniation. This might serve as a bridging therapy before orthotopic liver retransplantation (reOLT). Three patients after a first liver transplantation became candidate for urgent MARS treatment as a bridging solution prior to reOLT in our center. Authors report these three cases, focusing on indications, MARS sessions, clinical courses, and final outcomes.
Coexisting intrarenal arteriovenous and caliceovenous fistulae after percutaneous nephrolithotomy: Case report and literature review
Authors: Rastogi Neeraj , Zawacki Walter , Alencar Herlen 
Published: July 2013

Abstract
A 58-year-old man was re-admitted to the Urology service with delayed gross hematuria and unstable hemodynamics, following a percutaneous nephrolithotomy (PCNL) procedure performed for an obstructive solitary left lower calyceal stone. A selective left renal angiogram demonstrated an interpolar arteriovenous fistula (AVF), which was treated with successful coil embolization of a sub-segmental feeding branch. Subsequent nephrostogram confirmed a coexisting caliceovenous fistula, which was observed and healed spontaneously. Iatrogenic coexisting intrarenal AVF and caliceovenous fistulae have never been reported and should be considered as a possible cause of delayed severe hematuria with unstable hemodynamics, and/or increase in baseline creatinine after PCNL.
Red flags in bedside ultrasonography for surgical cases
Authors: Ünlüer Erden Erol , Karagöz Arif 
Published: July 2013

Abstract
Bedside ultrasonography is highly accurate in evaluating hypotension, even if performed by nonradiologist. Here we report three cases presenting with hypotension to the trauma room. In the first case, limited bedside ultrasonography demonstrated dilatation of the inferior vena cava and loss of respiratory variation in diameter. In further evaluation, dilated aortic root, massive pericardial effusion, collapse of right heart chambers, and a dissection flap at the anterior wall of base of ascending aorta were detected. With these findings, the patient was sent to the operation room with a diagnosis of DeBakey type 2 aortic dissection in approximately 15 min. In the second case, bedside ultrasonography demonstrated absence of pleural movements and comet tail artifacts on the right lung region of the patient. Together with deterioration of the vital signs, the patient was diagnosed as right-sided pneumothorax and underwent the tube thoracostomy. In the third case, bedside ultrasonography revealed the presence of free fluid in Morrison's pouch and splenorenal space in a hypotensive patient with a blunt abdominal trauma. He was consulted with general surgery department and was sent to the operation room without further diagnostic evaluation. In these cases, we emphasized the key role of bedside ultrasonography in hypotensive patients.
Integration of GaAs on Ge/Si towers by MOVPE
Authors: Taboada A. G. , Kreiliger T. , Falub C. V. , Richter M. , Isa F. , Müller E. , Uccelli E. , Niedermann P. , Neels A. , Isella G. , Fompeyrine J. , Dommann A. , von Känel H. 
Published: July 2013

ABSTRACTWe report on the maskless integration of micron-sized GaAs crystals on patterned Si substrates by metal organic vapor phase epitaxy. In order to adapt the mismatch between the lattice parameter and thermal expansion coefficient of GaAs and Si, 2 μm tall Ge crystals were first grown as virtual substrate by low energy plasma enhanced chemical vapor deposition. We investigate the morphological evolution of the GaAs structures grown on top of the Ge crystals at the transition towards full pyramids with energetically stable {111} facets. A substantial release of strain is shown in GaAs crystals with a height of 2 μm and lateral sizes up to 15×15 μm2 by both X-ray diffraction and photoluminescence.