bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of macrophage migration inhibitory factor and mannose-binding lectin-2 gene polymorphisms in acute rheumatic fever
Authors: Col-Araz Nilgun , Pehlivan Sacide , Baspinar Osman , Sever Tugce , Oguzkan-Balci Sibel , Balat Ayse 
Published: July 2012

AbstractBackgroundMacrophage migration inhibitory factor and mannose-binding lectin-2 play important roles in the pathogenesis of several acute and chronic inflammatory/autoimmune disorders. The aim of the study was to investigate any possible association between migration inhibitory factor and mannose-binding lectin-2 gene polymorphisms and acute rheumatic fever in children.Material and methodsA total of 38 unrelated children with acute rheumatic fever and 40 age- and sex-matched healthy controls were analysed for codon 54 A/B polymorphism in mannose-binding lectin-2 gene and −173 G/C polymorphism in migration inhibitory factor gene by using the polymerase chain reaction method.ResultsFrequency of BB genotype of mannose-binding lectin-2 gene was higher in the patient group. Interestingly, children with acute rheumatic fever with AA genotype tended to have chorea compared with children with BB genotype. There was a statistically significant increase in frequency of the migration inhibitory factor −173 CC genotype in patients compared with the control subjects.ConclusionThe present study is the first to investigate the mannose-binding lectin-2gene polymorphism in children with acute rheumatic fever. BB genotype of mannose-binding lectin-2 (codon 54) and CC genotype of migration inhibitory factor (−173) may have a role in the immunoinflammatory process of acute rheumatic fever.
Treatment of haemoptysis in pulmonary atresia with tranexamic acid
Authors: Devine Matthew J. , Radford Dorothy J. 
Published: July 2012

AbstractWe report the case of a young woman with continuing haemoptysis, pulmonary atresia, previous shunt surgery, and pulmonary hypertension. She was not suitable for further surgery or for therapeutic embolisation of bronchial vessels. Treatment with tranexamic acid resolved the haemoptysis.
Quantifying Cumulative Entrainment Effects for Chinook Salmon in a Heavily Irrigated Watershed
Authors: Walters Annika W. , Holzer Damon M. , Faulkner James R. , Warren Charles D. , Murphy Patrick D. , McClure Michelle M. 
Published: July 2012

AbstractPacific salmon Oncorhynchus spp. experience multiple small‐scale disturbances throughout their freshwater habitat, but the cumulative effect of these disturbances is often not known or not easily quantifiable. One such disturbance is water diversions, which can entrain fish and alter streamflow regimes. Threatened Lemhi River (Idaho) Chinook salmon O. tshawytscha smolts encounter 41–71 water diversions during their out‐migration. We used passive integrated transponder tag data to model the entrainment rate of Chinook salmon smolts as a function of the proportion of water removed by an irrigation diversion. Under median‐streamflow conditions with unscreened diversions, the estimated cumulative effect of the diversions was a loss of 71.1% of out‐migrating smolts due to entrainment. This is a large potential source of mortality, but screening is an effective mitigation strategy, as estimated mortality was reduced to 1.9% when all diversions were screened. If resources are limited, targeting the diversions that remove a large amount of water and diversions in locations with high fish encounter rates is most effective. Our modeling approach could be used to quantify the entrainment effects of water diversions and set screening priorities for other watersheds.
Metabolite identification and molecular fingerprint prediction through machine learning
Authors: Heinonen Markus , Shen Huibin , Zamboni Nicola , Rousu Juho 
Published: July 2012

Abstract
Motivation: Metabolite identification from tandem mass spectra is an important problem in metabolomics, underpinning subsequent metabolic modelling and network analysis. Yet, currently this task requires matching the observed spectrum against a database of reference spectra originating from similar equipment and closely matching operating parameters, a condition that is rarely satisfied in public repositories. Furthermore, the computational support for identification of molecules not present in reference databases is lacking. Recent efforts in assembling large public mass spectral databases such as MassBank have opened the door for the development of a new genre of metabolite identification methods.
Results: We introduce a novel framework for prediction of molecular characteristics and identification of metabolites from tandem mass spectra using machine learning with the support vector machine. Our approach is to first predict a large set of molecular properties of the unknown metabolite from salient tandem mass spectral signals, and in the second step to use the predicted properties for matching against large molecule databases, such as PubChem. We demonstrate that several molecular properties can be predicted to high accuracy and that they are useful in de novo metabolite identification, where the reference database does not contain any spectra of the same molecule.
Availability: An Matlab/Python package of the FingerID tool is freely available on the web at http://www.sourceforge.net/p/fingerid.
Contact: markus.heinonen@cs.helsinki.fi
imDEV: a graphical user interface to R multivariate analysis tools in Microsoft Excel
Authors: Grapov Dmitry , Newman John W. 
Published: July 2012

AbstractSummary: Interactive modules for Data Exploration and Visualization (imDEV) is a Microsoft Excel spreadsheet embedded application providing an integrated environment for the analysis of omics data through a user-friendly interface. Individual modules enables interactive and dynamic analyses of large data by interfacing R's multivariate statistics and highly customizable visualizations with the spreadsheet environment, aiding robust inferences and generating information-rich data visualizations. This tool provides access to multiple comparisons with false discovery correction, hierarchical clustering, principal and independent component analyses, partial least squares regression and discriminant analysis, through an intuitive interface for creating high-quality two- and a three-dimensional visualizations including scatter plot matrices, distribution plots, dendrograms, heat maps, biplots, trellis biplots and correlation networks.Availability and implementation: Freely available for download at http://sourceforge.net/projects/imdev/. Implemented in R and VBA and supported by Microsoft Excel (2003, 2007 and 2010).Contact: John.Newman@ars.usda.govSupplementary Information: Installation instructions, tutorials and users manual are available at http://sourceforge.net/projects/imdev/.
Quantifying uniformity of mapped reads
Authors: Hower Valerie , Starfield Richard , Roberts Adam , Pachter Lior 
Published: July 2012

Abstract
Summary: We describe a tool for quantifying the uniformity of mapped reads in high-throughput sequencing experiments. Our statistic directly measures the uniformity of both read position and fragment length, and we explain how to compute a P-value that can be used to quantify biases arising from experimental protocols and mapping procedures. Our method is useful for comparing different protocols in experiments such as RNA-Seq.
Availability and implementation: We provide a freely available and open source python script that can be used to analyze raw read data or reads mapped to transcripts in BAM format at http://www.math.miami.edu/~vhower/ReadSpy.html
Contact: lpachter@math.berkeley.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
Marked Hyperglycemia Attenuates Anesthetic Preconditioning in Human-induced Pluripotent Stem Cell-derived Cardiomyocytes
Authors: Canfield Scott G. , Sepac Ana , Sedlic Filip , Muravyeva Maria Y. , Bai Xiaowen , Bosnjak Zeljko J. 
Published: July 2012

Introduction
Anesthetic preconditioning protects cardiomyocytes from oxidative stress-induced injury, but it is ineffective in patients with diabetes mellitus. To address the role of hyperglycemia in the inability of diabetic individuals to be preconditioned, we used human cardiomyocytes differentiated from induced pluripotent stem cells generated from patients with or without type 2 diabetes mellitus (DM-iPSC- and N-iPSC-CMs, respectively) to investigate the efficacy of preconditioning in varying glucose conditions (5, 11, and 25 mM).

Methods
Induced pluripotent stem cells were induced to generate cardiomyocytes by directed differentiation. For subsequent studies, cardiomyocytes were identified by genetic labeling with enhanced green fluorescent protein driven by a cardiac-specific promoter. Cell viability was analyzed by lactate dehydrogenase assay. Confocal microscopy was utilized to measure opening of the mitochondrial permeability transition pore and the mitochondrial adenosine 5'-triphosphate-sensitive potassium channels.

Results
Isoflurane (0.5 mM) preconditioning protected N-iPSC- and DM-iPSC-CMs from oxidative stress-induced lactate dehydrogenase release and mitochondrial permeability transition pore opening in 5 mM and 11 mM glucose. Isoflurane triggered mitochondrial adenosine-5'-triphosphate-sensitive potassium channel opening in N-iPSC-CMs in 5 mM and 11 mM glucose and in DM-iPSC-CMs in 5 mM glucose; 25 mM glucose disrupted anesthetic preconditioning-mediated protection in DM-iPSC- and N-iPSC-CMs.

Conclusions
The opening of mitochondrial adenosine 5'-triphosphate-sensitive potassium channels are disrupted in DM-iPSC-CMs in 11 mM and 25 mM glucose and in N-iPSC-CMs in 25 mM glucose. Cardiomyocytes derived from healthy donors and patients with a specific disease, such as diabetes in this study, open possibilities in studying genotype- and phenotype-related pathologies in a human-relevant model.
Sodium Nitrite Mitigates Ventilator-induced Lung Injury in Rats
Authors: Pickerodt Philipp A. , Emery Michael J. , Zarndt Rachel , Martin William , Francis Roland C. E. , Boemke Willehad , Swenson Erik R. 
Published: July 2012

Background
Nitrite (NO2) is a physiologic source of nitric oxide and protects against ischemia-reperfusion injuries. We hypothesized that nitrite would be protective in a rat model of ventilator-induced lung injury and sought to determine if nitrite protection is mediated by enzymic catalytic reduction to nitric oxide.

Methods
Rats were anesthetized and mechanically ventilated. Group 1 had low tidal volume ventilation (LVT) (6 ml/kg and 2 cm H2O positive end-expiratory pressure; n=10); group 2 had high tidal volume ventilation (HVT) (2 h of 35 cm H2O inspiratory peak pressure and 0 cm H2O positive end-expiratory pressure; n=14); groups 3-5: HVT with sodium nitrite (NaNO2) pretreatment (0.25, 2.5, 25 μmol/kg IV; n=6-8); group 6: HVT+NaNO2+nitric oxide scavenger 2-(4-carboxyphenyl)-4,5dihydro-4,4,5,5-tetramethyl-1H-imidazolyl-1-oxy-3oxide(n=6); group 7: HVT+NaNO2+nitric oxide synthase inhibitor N-nitro-L-arginine methyl ester (n=7); and group 8: HVT+NaNO2+xanthine oxidoreductase inhibitor allopurinol (n=6). Injury assessment included physiologic measurements (gas exchange, lung compliance, lung edema formation, vascular perfusion pressures) with histologic and biochemical correlates of lung injury and protection.

Results
Injurious ventilation caused statistically significant injury in untreated animals. NaNO2 pretreatment mitigated the gas exchange deterioration, lung edema formation, and histologic injury with maximal protection at 2.5 μmol/kg. Decreasing nitric oxide bioavailability by nitric oxide scavenging, nitric oxide synthase inhibition, or xanthine oxidoreductase inhibition abolished the protection by NaNO2.

Conclusions
Nitrite confers protection against ventilator-induced lung injury in rats. Catalytic reduction to nitric oxide and mitigation of ventilator-induced lung injury is dependent on both xanthine oxidoreductase and nitric oxide synthases.
Roles of Gr-1+Leukocytes in Postincisional Nociceptive Sensitization and Inflammation
Authors: Sahbaie Peyman , Li Xiangqi , Shi Xiaoyou , Clark J. David 
Published: July 2012

Background
Neutrophils are one of the predominant immune cells initially migrating to surgical wound edges. They produce mediators both associated with supporting (interleukin [IL]-1β, C5a) and reducing (opioid peptides) pain. Studies demonstrate neutrophil depletion/blockade reduces nociceptive sensitization after nerve injury and carrageenan administration, but enhance sensitization in complete Freund's adjuvant inflammation. This research identifies the contribution of infiltrating neutrophils to incisional pain and inflammation.

Methods
Antibody-mediated Gr1 neutrophil depletion preceded hind paw incisions. Sensitization to mechanical and thermal stimuli, effects on edema and local levels of IL-1β and C5a were measured. Local effects of C5a or IL-1 receptor antagonists PMX-53 and anakinra on sensitization after neutrophil depletion were examined. Groups of 4-8 mice were used.

Results
Anti-Gr1 antibody depleted more than 90% of circulating and infiltrating skin neutrophils after incision. Neutrophil depletion did not change magnitude or duration of mechanical hypersensitivity in incised mice. However, paw edema was significantly reduced and heat hypersensitivity was slightly increased in depleted animals. In depleted animals IL-1β levels were half of controls 24 h after incision, whereas C5a levels were increased in both. Prominent IL-1β immunohistochemical staining of epidermis was seen in both groups. PMX-53 and anakinra reduced incisional mechanical and heat nociceptive sensitization to the same extent, regardless of neutrophil depletion.

Conclusions
Neutrophil-derived IL-1β and C5a do not appear to contribute critically to peri-incisional nociceptive signaling. Other sources of mediators, such as epidermal cells, may need to be considered. Controlling inflammatory activation of resident cells in epidermis/deeper structures may show therapeutic efficacy in reducing pain from surgical incisions.
Serotype‐dependent expression patterns of stabilized lipopolysaccharide aggregates in Aggregatibacter actinomycetemcomitans strains
Authors: Kikuchi Haruko , Fujise Osamu , Miura Mayumi , Tanaka Ayako , Hisano Kyoko , Haraguchi Akira , Hamachi Takafumi , Maeda Katsumasa 
Published: July 2012

ABSTRACTAbove a critical concentration, amphiphilic lipopolysaccharide (LPS) molecules in an aqueous environment form aggregate structures, probably because of interactions involving hydrophobic bonds. Ionic bonds involving divalent cations stabilize these aggregate structures, making them resistant to breakdown by detergents. The aim of this study was to examine expression patterns of stabilized LPS aggregates in Aggregatibacter actinomycetemcomitans, a microorganism that causes periodontitis. A. actinomycetemcomitans strains of various serotypes and truncated LPS mutants were prepared for this study. Following treatment with a two‐phase separation system using the detergent Triton X‐114, crude LPS extracts of the study strains were separated into detergent‐phase LPS (DP‐LPS) and aqueous‐phase LPS (AP‐LPS). Repeated treatment of the aqueous phase with the two‐phase separation system produced only a slight decrease in AP‐LPS, suggesting that AP‐LPS was resistant to the detergent and thus distinguishable from DP‐LPS. The presence of divalent cations increased the yield of AP‐LPS. AP‐LPS expression patterns were serotype‐dependent; serotypes b and f showing early expression, and serotypes a and c late expression. In addition, highly truncated LPS from a waaD (rfaD) mutant were unable to generate AP‐LPS, suggesting involvement of the LPS structure in the generation of AP‐LPS. The two‐phase separation was able to distinguish two types of LPS with different physical states at the supramolecular structure level. Hence, AP‐LPS likely represents stabilized LPS aggregates, whereas DP‐LPS might be derived from non‐stabilized aggregates. Furthermore, time‐dependent expression of stabilized LPS aggregates was found to be serotype‐dependent in A. actinomycetemcomitans.
Neuropsychiatric events in varenicline and nicotine replacement patch users in the Military Health System
Authors: Meyer Tamra E. , Taylor Lockwood G. , Xie Suji , Graham David J. , Mosholder Andrew D. , Williams James R. , Moeny David , Ouellet‐Hellstrom Rita P. , Coster Trinka S. 
Published: July 2012

AbstractAimTo determine the rate ratio of neuropsychiatric hospitalizations in new users of varenicline compared to new users of nicotine replacement therapy (NRT) patch in the Military Health System (MHS).Design, setting and participantsVarenicline (n = 19 933) and NRT patch (n = 15 867) users who initiated therapy from 1 August 2006 to 31 August 2007 within the MHS were included in this retrospective cohort study. After matching according to propensity scores, 10 814 users remained in each cohort. The study population included those with and without a history of neuropsychiatric disease.MeasurementsPatients were followed for neuropsychiatric hospitalizations defined by primary neuropsychiatric discharge diagnosis using ICD‐9 codes from in‐patient administrative claims. Hazard ratios (HR) and 95% confidence intervals (CI) were estimated after propensity score matching on exposure for socio‐demographic factors, health‐care utilization, comorbidities, medication history and neuropsychiatric history.FindingsThere was no increase in the rate of neuropsychiatric hospitalizations in patients treated with varenicline compared to NRT patch when followed for 30 days (propensity‐score matched HR = 1.14, 95% CI: 0.56–2.34). Results were similar after 60 days of follow‐up.ConclusionsThere does not appear to be an increase in neuropsychiatric hospitalizations with varenicline compared with nicotine replacement therapy patch over 30 or 60 days after drug initiation.
Polymorphism identification in goat GNRH1 and GDF9 genes and their association analysis with litter size
Authors: An X. P. , Hou J. X. , Zhao H. B. , Li G. , Bai L. , Peng J. Y. , M Yan Q. , Song Y. X. , Wang J. G. , Cao B. Y. 
Published: July 2012

SummaryThis study investigated the polymorphisms of
GNRH1 and GDF9 genes in 641 goats of three breeds: Xinong Saanen, Guanzhong and Boer. Two allelic variants were identified in the GNRH1 gene (JN645280:g.3548A>G and JN645281:g.3699G>A) and one allelic variant was found in the GDF9 gene (JN655693:g.4093G>A). Furthermore, g.4093G>A was a missense mutation (p.Val397Ile of GDF9). Results of an association analysis indicated that SNPs g.3548A>G and g.4093G>A had significant effects on litter size (P < 0.05). The combination genotypes of SNPs g.3548A>G, g.3699G>A and g.4093G>A also affected litter size with the C5 genotype having the highest litter size in the first, third, fourth and average parity. Hence, the biochemical and physiological functions, together with the results obtained in our investigation, suggest that the GNRH1 and
GDF9 genes could serve as genetic markers for litter size in goat breeding.
Intrinsic factors affecting adequacy of thyroid nodule fine‐needle aspiration cytology
Authors: Grani Giorgio , Calvanese Anna , Carbotta Giovanni , D'Alessandri Mimma , Nesca Angela , Bianchini Marta , Sordo Marianna Del , Fumarola Angela 
Published: July 2012

SummaryObjectiveTo evaluate intrinsic nodule features predictive of an inadequate report in fine‐needle aspiration cytology (FNAC).DesignSingle‐centre cross‐sectional study.MethodsBetween May 2005 and April 2011, 3279 ultrasonography‐assisted FNACs were carried out and features of nodules recorded prospectively. Univariate logistic regression analyses were performed to estimate the association between nondiagnostic cytology and variables such as age, gender, single nodule, maximum nodule diameter and estimated volume.ResultsInadequate or nondiagnostic samples were reported in 1195 FNACs. All diameters were found to be predictors of nondiagnostic cytology; estimated nodule volume, on the other hand, was not. Nodules with a diameter <10 mm were more frequently nondiagnostic (OR 1·65, 95% CI 1·40–1·94, P < 0·001). Neither micro‐ nor macrocalcification increased the risk of inadequacy. On the contrary, mixed lesions were more frequently diagnostic (OR 0·68, 95% CI 0·85–0·80, P < 0·001). Solid nodule aspiration was performed more easily on isoechogenic nodules (OR 0·64, 95% CI 0·54–0·77, P < 0·001); the same procedure was more cumbersome on hypoechogenic lesions (OR 1·87, 95% CI 1·62–2·16, P < 0·001). Increased vascularization did not cause a significant increase in the nondiagnostic results. Blurred margins increased the inadequacy rate (OR 1·45, 95% CI 1·24–1·69, P < 0·001), while presence of a hypoechogenic halo decreased it (OR 0·67, 95% CI 0·54–0·82, P < 0·001).ConclusionsSome ultrasonographic features suggestive of malignancy may be predictive of inadequate cytology. Patients must be notified that the FNA report may be nondiagnostic and that this represents a limitation of the technique related to the structure of lesions.
Coherent and random noise attenuation via multichannel singular spectrum analysis in the randomized domain
Authors: Chiu Stephen K. 
Published: July 2012

ABSTRACTThe attenuation of coherent and random noise still poses technical challenges in seismic data processing, especially in onshore environments. Multichannel Singular Spectrum Analysis (MSSA) is an existing and effective technique for random‐noise reduction. By incorporating a randomizing operator into MSSA, this modification creates a new and powerful filtering method that can attenuate both coherent and random noise simultaneously. The key of the randomizing operator exploits the fact that primary events after NMO are relatively horizontal. The randomizing operator randomly rearranges the order of input data and reorganizes coherent noise into incoherent noise but has a minimal effect on nearly horizontal primary reflections. The randomizing process enables MSSA to suppress both coherent and random noise simultaneously. This new filter, MSSARD (MSSA in the randomized domain) also resembles a combination of eigenimage and Cadzow filters. I start with a synthetic data set to illustrate the basic concept and apply MSSARD filtering on a 3D cross‐spread data set that was severely contaminated with ground roll and scattered noise. MSSARD filtering gives superior results when compared with a conventional 3D f‐k filter. For a random‐noise example, the application of MSSARD filtering on time‐migrated offset‐vector‐tile (OVT) gathers also produces images with higher signal‐to‐noise ratios than a conventional f‐xy deconvolution filter.