bluuebunny/crossref_metadata_2025_split huggingface dataset:
New resonant LCL boost converter
Authors: Jabbari Masoud , Barati Fateme 
Published: July 2014

This study presents a new soft‐switching resonant step‐up converter. An auxiliary high‐frequency resonant LC tank along with a switch constitute the auxiliary network added to the classic pulse width modulation (PWM) boost converter. Size of the main inductor of boost converter is also reduced, so that in conjunction with the auxiliary LC tank forms an LCL resonant network. This network provides zero‐current switching (ZCS) conditions for both switches independent from the load‐current and operating voltages. The converter can operate at ZCS in discontinuous conduction mode, continuous conduction mode (CCM) and deep‐CCM depending on the switching frequency; and, at deep‐CCM, the current stresses are minimised. Experimental results from a 100 W/100 kHz laboratory prototype verify the integrity of the presented theoretical analysis.
High‐efficiency battery charger with cascode output design
Authors: Chiu Huang‐Jen , Lo Yu‐Kang , Tseng Po‐Jung , Liu Yu‐Chen 
Published: July 2014

This study presents a high‐efficiency battery charger with cascode output design. The output voltage is cascode comprising two parts: one is fixed and the other is variable. High efficiency can be achieved under a wide range of output voltage variations. This topology can increase the utilisation of transformer duty cycle and reduce the power loss. The constant current and constant voltage charging schemes can be achieved by the proposed cascode configuration for battery charger applications. A 3.3 kW laboratory prototype is implemented and tested. The experimental results verify the feasibility of the proposed scheme.
Line current harmonics of three‐level neutral‐point‐clamped electric multiple unit rectifiers: analysis, simulation and testing
Authors: Kejian Song , Mingli Wu , Agelidis Vassilios Georgios , Hui Wang 
Published: July 2014

The harmonic spectra of the AC supply currents of electric multiple units (EMUs) employing three‐level neutral‐point‐clamped converters are discussed in this study. The analytical expressions of high‐order harmonics because of high‐frequency three‐level phase‐opposition disposition pulse‐width modulation are derived by using double Fourier series and a contour plot in a two‐dimensional plane. The carrier phase‐shift control to cancel some of the high‐order harmonics when two or more converters are interlaced is validated. The impact of converter's DC voltage controller on low‐order harmonics is formulated. The harmonic spectra are verified by computer simulations and through actual measured data taken at lower train speed and rated power from an EMU of the CRH380AL and tested on a 9 km long testing railway line in a purpose built rolling stocks plant.
Tie-Intertextuality, or, Intertextuality as Incorporation in the Tie-in Merchandise to Disney’sAlice in Wonderland(2010)
Authors: Elliott Kamilla 
Published: July 2014

AbstractTie-in merchandise for Walt Disney’s and Tim Burton’s film, Alice in Wonderland (2010), dislocates and modifies prior theories of intertextuality in adaptation studies with the intertextual practices of corporate entertainment franchises. Poststructuralist and postmodern theories of intertextuality construct it as a subversive and democratizing operation, dispersing meaning among texts, dismantling high/low art hierarchies, and redistributing interpretive authority among artists, professional critics, and ordinary audiences. Even when tie-in merchandise for the Disney-Burton film is subversive of mainstream Disney aesthetics and ideologies, Disney and its licensed tie-in merchandising affiliates engage in rhetoric and practices that reincorporate dispersed and contesting intertexts, producing a portmanteau of ‘tie-intertextuality’. Consumers as well as products are tied in or incorporated as corporate intertexts through a rhetoric and iconography of acting, interactivity, inspiration, incarnation, and fidelity. The effect is more one of capitalist dialogics than of the Marxist dialectics academics have traditionally championed in theories of intertextuality.
Fast and accurate imputation of summary statistics enhances evidence of functional enrichment
Authors: Pasaniuc Bogdan , Zaitlen Noah , Shi Huwenbo , Bhatia Gaurav , Gusev Alexander , Pickrell Joseph , Hirschhorn Joel , Strachan David P. , Patterson Nick , Price Alkes L. 
Published: July 2014

Abstract
Motivation: Imputation using external reference panels (e.g. 1000 Genomes) is a widely used approach for increasing power in genome-wide association studies and meta-analysis. Existing hidden Markov models (HMM)-based imputation approaches require individual-level genotypes. Here, we develop a new method for Gaussian imputation from summary association statistics, a type of data that is becoming widely available.
Results: In simulations using 1000 Genomes (1000G) data, this method recovers 84% (54%) of the effective sample size for common (&gt;5%) and low-frequency (1–5%) variants [increasing to 87% (60%) when summary linkage disequilibrium information is available from target samples] versus the gold standard of 89% (67%) for HMM-based imputation, which cannot be applied to summary statistics. Our approach accounts for the limited sample size of the reference panel, a crucial step to eliminate false-positive associations, and it is computationally very fast. As an empirical demonstration, we apply our method to seven case–control phenotypes from the Wellcome Trust Case Control Consortium (WTCCC) data and a study of height in the British 1958 birth cohort (1958BC). Gaussian imputation from summary statistics recovers 95% (105%) of the effective sample size (as quantified by the ratio of χ2 association statistics) compared with HMM-based imputation from individual-level genotypes at the 227 (176) published single nucleotide polymorphisms (SNPs) in the WTCCC (1958BC height) data. In addition, for publicly available summary statistics from large meta-analyses of four lipid traits, we publicly release imputed summary statistics at 1000G SNPs, which could not have been obtained using previously published methods, and demonstrate their accuracy by masking subsets of the data. We show that 1000G imputation using our approach increases the magnitude and statistical evidence of enrichment at genic versus non-genic loci for these traits, as compared with an analysis without 1000G imputation. Thus, imputation of summary statistics will be a valuable tool in future functional enrichment analyses.
Availability and implementation: Publicly available software package available at http://bogdan.bioinformatics.ucla.edu/software/ .
Contact: bpasaniuc@mednet.ucla.edu or aprice@hsph.harvard.edu
Supplementary information: Supplementary materials are available at Bioinformatics online.
cc
SOL
omics
: a webserver for solubility prediction of endogenous and heterologous expression in
Escherichia coli
Authors: Agostini Federico , Cirillo Davide , Livi Carmen Maria , Delli Ponti Riccardo , Tartaglia Gian Gaetano 
Published: July 2014

Abstract
Summary: Here we introduce cc SOL omics , a webserver for large-scale calculations of protein solubility. Our method allows (i) proteome-wide predictions; (ii) identification of soluble fragments within each sequences; (iii) exhaustive single-point mutation analysis.
Results: Using coil/disorder, hydrophobicity, hydrophilicity, β-sheet and α-helix propensities, we built a predictor of protein solubility. Our approach shows an accuracy of 79% on the training set (36 990 Target Track entries). Validation on three independent sets indicates that ccSOL omics discriminates soluble and insoluble proteins with an accuracy of 74% on 31 760 proteins sharing &lt;30% sequence similarity.
Availability and implementation: cc SOL omics can be freely accessed on the web at http://s.tartaglialab.com/page/ccsol_group . Documentation and tutorial are available at http://s.tartaglialab.com/static_files/shared/tutorial_ccsol_omics.html .
Contact: gian.tartaglia@crg.es
Supplementary information: Supplementary data are available at Bioinformatics online.
Intensity drift removal in LC/MS metabolomics by common variance compensation
Authors: Fernández-Albert Francesc , Llorach Rafael , Garcia-Aloy Mar , Ziyatdinov Andrey , Andres-Lacueva Cristina , Perera Alexandre 
Published: July 2014

Abstract
Liquid chromatography coupled to mass spectrometry (LC/MS) has become widely used in Metabolomics. Several artefacts have been identified during the acquisition step in large LC/MS metabolomics experiments, including ion suppression, carryover or changes in the sensitivity and intensity. Several sources have been pointed out as responsible for these effects. In this context, the drift effects of the peak intensity is one of the most frequent and may even constitute the main source of variance in the data, resulting in misleading statistical results when the samples are analysed. In this article, we propose the introduction of a methodology based on a common variance analysis before the data normalization to address this issue. This methodology was tested and compared with four other methods by calculating the Dunn and Silhouette indices of the quality control classes. The results showed that our proposed methodology performed better than any of the other four methods. As far as we know, this is the first time that this kind of approach has been applied in the metabolomics context.
Availability and implementation: The source code of the methods is available as the R package intCor at http://b2slab.upc.edu/software-and-downloads/intensity-drift-correction/ .
Supplementary information: Supplementary data are available at Bioinformatics online.
Cathelicidin rCRAMP stimulates rat mast cells to generate cysteinyl leukotrienes, synthesize TNF and migrate: involvement of PLC/A2, PI3K and MAPK signaling pathways
Authors: Bąbolewska Edyta , Pietrzak Anna , Brzezińska-Błaszczyk Ewa 
Published: July 2014

AbstractCathelicidins represent a family of cationic peptides involved in host defense systems. Apart from exerting direct anti-microbial effects, cathelicidins can regulate immune responses by affecting the activity of cells playing a role in antibacterial defense. Taking into account that mast cells are critical components of host defense, the aim of this study was to determine whether rat cathelicidin-related anti-microbial peptide (rCRAMP) can influence mast cell activity. We have demonstrated that activation of fully mature rat mast cells with rCRAMP resulted in generation and release of cysteinyl leukotrienes (cysLTs). However, rCRAMP failed to induce mast cell degranulation and histamine release. We also found that rCRAMP stimulated rat mast cells to synthesize TNF, but not CXCL8. What is more, this peptide induced GM-CSF, IL-1β, CCL2 and CCL3 but not IL-33 mRNA expression in mast cells. Finally, we showed that this cathelicidin serves as potent chemoattractant for rat mast cells. rCRAMP-mediated cysLT synthesis and mast cell migration were strongly inhibited by IL-10 pre-treatment. With the use of specific inhibitors, we established that activation of PLC/A2 and ERK1/2, but not p38, was required for rCRAMP-induced mast cell stimulation, while PI3K-dependent pathway is involved in both TNF synthesis and mast cell migration. Our results suggest that cathelicidins can amplify inflammatory responses by causing mast cells accumulation and by stimulating these cells to release potent pro-inflammatory mediators.
Exquisite allele discrimination by toehold hairpin primers
Authors: Byrom Michelle , Bhadra Sanchita , Jiang Yu Sherry , Ellington Andrew D. 
Published: July 2014

Abstract
The ability to detect and monitor single nucleotide polymorphisms (SNPs) in biological samples is an enabling research and clinical tool. We have developed a surprising, inexpensive primer design method that provides exquisite discrimination between SNPs. The field of DNA computation is largely reliant on using so-called toeholds to initiate strand displacement reactions, leading to the execution of kinetically trapped circuits. We have now similarly found that the short toehold sequence to a target of interest can initiate both strand displacement within the hairpin and extension of the primer by a polymerase, both of which will further stabilize the primer:template complex. However, if the short toehold does not bind, neither of these events can readily occur and thus amplification should not occur. Toehold hairpin primers were used to detect drug resistance alleles in two genes, rpoB and katG, in the Mycobacterium tuberculosis genome, and ten alleles in the Escherichia coli genome. During real-time PCR, the primers discriminate between mismatched templates with Cq delays that are frequently so large that the presence or absence of mismatches is essentially a ‘yes/no’ answer.
Calcitonin Gene–related Peptide Is Involved in Inflammatory Pain but Not in Postoperative Pain
Authors: Ishida Kumiko , Kawamata Tomoyuki , Tanaka Satoshi , Shindo Takayuki , Kawamata Mikito 
Published: July 2014

Abstract

Background:
The aim of this study was to clarify the roles of calcitonin gene–related peptide (CGRP) in postoperative pain and inflammatory pain.

Methods:
αCGRP knockout mice that the authors have developed and wild-type mice were used. Pain behaviors were assessed after incision and complete Freund’s adjuvant (CFA) injection. Changes in CGRP and c-Fos expression in the dorsal horn were also examined.

Results:
Guarding pain scores in αCGRP knockout mice were lower than those in wild-type mice at 24 h (3.8 ± 1.6 vs. 6.8 ± 1.5, P = 0.044) and 48 h (1.8 ± 1.7 vs. 6.0 ± 1.5, P = 0.001) after CFA injection (n = 8 to 9). Withdrawal latencies to heat stimulation in αCGRP knockout mice were higher than those in wild-type mice at 24 to 72 h after CFA injection (4.9 ± 1.0 vs. 3.4 ± 0.8 at 24 h, P = 0.04; 5.1 ± 0.3 vs. 3.2 ± 0.9 at 48 h, P = 0.047; and 5.4 ± 1.6 vs. 3.5 ± 0.5 s at 72 h, P = 0.045) (n = 11 to 13), but withdrawal thresholds to mechanical stimulation were comparable. CGRP expression was increased at 24 h after CFA injection in wild-type mice, and the c-Fos–positive profile was increased at 4 h after CFA injection (ipsilateral vs. contralateral: 12.3 ± 4.6 vs. 1.3 ± 1.9, P < 0.0001) and maintained at 24 h (10.0 ± 4.1 vs. 0.8 ± 1.3, P < 0.0001) (n = 4 to 6).

Conclusion:
These results suggest that contribution of the αCGRP system depends on the modality of pain and the stage of inflammation.
Endocrine and Neurobehavioral Abnormalities Induced by Propofol Administered to Neonatal Rats
Authors: Tan Sijie , Xu Changqing , Zhu Wanting , Willis Jesse , Seubert Christoph N. , Gravenstein Nikolaus , Sumners Colin , Martynyuk Anatoly E. 
Published: July 2014

Abstract

Background:
The authors studied whether neonatal propofol anesthesia affects development of the endocrine and neural systems.

Methods:
Sprague–Dawley rats were anesthetized using intraperitoneal propofol for 5 h on postnatal days (P) 4, 5, or 6. Pups that received either saline or intralipid, but not those in the negative control groups, were also maternally separated for 5 h. Serum levels of corticosterone were measured immediately after anesthesia and in adulthood after prepulse inhibition of acoustic startle testing (≥P80), followed by measurement of hippocampal neuronal activity.

Results:
Propofol acutely increased corticosterone levels to 146.6 ± 23.5 ng/ml (n = 6) versus 16.4 ± 3.5 ng/ml (n = 6) and 18.4 ± 3.2 ng/ml (n = 6) in saline- and intralipd-treated pups, respectively. In adulthood, the propofol group exhibited exacerbated endocrine responses to stress in a form of increased corticosterone levels (1,171.58 ± 149.17 ng/ml [n = 15] vs. 370.02 ± 36.01 ng/ml [n = 10] in the saline group). The propofol group had increased the frequency of miniature inhibitory postsynaptic currents in CA1 neurons of male and female rats, but reduced prepulse inhibition of startle was detected only in males. The Na+–K+–2Cl− cotransporter inhibitor bumetanide, administered to pups before propofol injection, alleviated long-term endocrine and prepulse inhibition abnormalities. Exogenous corticosterone, administered to naive pups, induced synaptic and endocrine but not prepulse inhibition effects, similar to those of propofol.

Conclusion:
Propofol-caused acute increases in corticosterone levels and γ-aminobutyric acid type A receptor–mediated excitation at the time of anesthesia may play mechanistic roles in development of exacerbated endocrine responses to stress and neurobehavioral abnormalities.
Vitamin and Zinc Status Pretreatment and Posttreatment in Patients With Inflammatory Bowel Disease
Authors: Santucci Neha R. , Alkhouri Razan H. , Baker Robert D. , Baker Susan S. 
Published: July 2014

ABSTRACTVitamin deficiencies are common in inflammatory bowel disease. Here we present 5‐year follow‐up data of 61 patients. No folate or vitamin B12 deficiency was identified throughout the study. A daily multivitamin supplement was sufficient to replete 100% of vitamin A–deficient and vitamin E–deficient patients. A total of 52% of vitamin D–deficient patients corrected, but 15% who had normal vitamin D levels at diagnosis developed deficiency. A total of 63% of zinc‐deficient patients normalized their zinc status, but 15% developed zinc deficiency at follow‐up despite supplementation.
Distinctive Colonic Mucosal Cytokine Signature in New‐Onset, Untreated Pediatric Crohn Disease
Authors: Sylvester Francisco A. , Draghi Andrew , Menoret Antoine , Fernandez Marina L. , Wang Zhu , Vella Anthony T. 
Published: July 2014

ABSTRACTObjective:The aim of the study was to compare the colonic mucosal immune response in children with new, untreated Crohn disease (CD‐New), CD in remission (CD‐Remission), and unaffected children (CTRL [controls]).Methods:We performed flow cytometry of mitogen‐stimulated colonic lamina propria mononuclear cells isolated from colonic biopsies and 72‐hour biopsy explant cultures, and analyzed the supernatant by an unbiased multiplex cytokine array of 45 analytes.Results:Thirty‐six children were studied (mean age 14 ± 3 years, 14 girls): 12 CD‐New, 11 CD‐Remission, and 13 CTRL. We found that stimulation of lamina propria mononuclear cells isolated from colonic biopsies induced comparable intracellular cytokine levels of interferon (IFN‐γ), interleukin (IL)‐17, and tumor necrosis factor (TNF)‐α in T cells from CD‐New, CD‐Remission, and CTRL, suggesting that mucosal innate inflammation plays a larger role than activated T cells in CD‐New. To measure factors released during the ongoing inflammatory response in CD‐New, we cultured colonic biopsy explants and uncovered 13/45 factors that were significantly higher in CD‐New versus CD‐Remission, whereas 10 were increased in CD‐New over CTRL. Ingenuity Pathway Analysis software revealed the anticipated interconnectivity of TNF‐α, IL‐6, and CSF‐2 in CD‐New of the colon. A novel subnetwork of chemokines was, however, evident, whereas IL‐17a appeared as a peripheral factor. Principal component analysis and hierarchal clustering showed that CD‐New and CD‐Remission separated into distinct subgroups based on the 13 factors.Conclusions:At diagnosis of inflammatory bowel disease, the colonic cytokine response contains a predominance of innate immune factors, with chemoattractants and vascular adhesion molecules playing a central role.
Outcome After Anal Intrasphincteric Botox Injection in Children With Surgically Treated Hirschsprung Disease
Authors: Han‐Geurts Ingrid J.M. , Hendrix Vivian C. , de Blaauw Ivo , Wijnen Marc H.W.A. , van Heurn Ernest L.W. 
Published: July 2014

ABSTRACTObjectives:A nonrelaxing internal anal sphincter is present in a relatively large proportion of children with surgically treated Hirschsprung disease (HD) and can cause obstructive gastrointestinal symptoms. The short‐ and long‐term outcome and adverse effects of intrasphincteric botulinum toxin (Botox) injections in children with obstruction after surgically treated HD are evaluated.Methods:The outcome of children with surgically treated HD treated with intrasphincteric Botox injections for obstructive symptoms was analyzed with a retrospective chart review between 2002 and 2013 in the University Medical Centers of Maastricht and Nijmegen.Results:A total of 33 patients were included. The median time of follow‐up was 7.3 years (range 1–24). A median of 2 (range 1–5) injections were given. Initial improvement was achieved in 76%, with a median duration of 4.1 months (range 1.7–58.8). Proportion of children hospitalized for enterocolitis decreased after treatment from 19 to 7. A good long‐term response was found in 49%. Two children experienced complications: transient pelvic muscle paresis with impairment of walking. In both children symptoms resolved within 4 months without treatment.Conclusions:Intrasphincteric Botox injections in surgically treated HD are an effective long‐term therapy in approximately half of our patients with obstructive symptoms. The possibility of adverse effects should be noticed.
Intractable Diarrhea of Infancy
Authors: Hizarcioglu‐Gulsen Hayriye , Saltik‐Temizel Inci N. , Demir Hulya , Gurakan Figen , Ozen Hasan , Yuce Aysel 
Published: July 2014

ABSTRACTObjectives:Intractable diarrhea of infancy (IDI), a group of prolonged diarrheal disorders, is difficult to diagnose and manage. We documented general features of patients and the causes of IDI.Methods:The present retrospective study included 60 hospitalized patients with IDI ages 0 to 24 months during January 2000 to December 2010. Detailed history, laboratory and endoscopic findings, diagnoses, and clinical courses were reviewed. Descriptive analyses were used for statistical evaluation.Results:The male/female ratio was 1.4. The median age at onset of diarrhea was 12 days. A total of 70% and 11% of patients were severely and moderately malnourished, respectively. Carbohydrate malabsorption (CM) and food allergies (n = 11, 18% for both) were the most frequent causes. A total of 16 of the patients (27%) did not have a specific diagnosis. The other diagnoses were infections (n = 5), immune‐mediated disorders (IMD) (n = 6), congenital enterocyte defects (CED) (n = 3, 5%), short bowel syndrome (n = 2), cystic fibrosis (n = 2), intestinal pseudoobstruction (n = 1), congenital disorder of glycosylation (n = 1), abetalipoproteinemia (n = 1), and proprotein convertase (PC) 1 deficiency (n = 1). Stool calprotectin level was high in 10 of 19 patients with Crohn disease (n = 3, mean 1116 ± 851 mg/L), food allergy (n = 4, mean 516 ± 288 mg/L), and undefined etiology (n = 3, mean 616 ± 780 mg/L). The mean duration of hospitalization was 76 days.Conclusions:IDI is a heterogenous group of diarrheal disorders. The most frequent causes were CM and food allergies in our study. Because high levels of calprotectin support inflammation, calprotectin levels may help to discriminate CED and inflammatory causes of IDI.
Bonsai: An event-based framework for processing and controlling data streams
Authors: Lopes Gonçalo , Bonacchi Niccolò , Frazão João , Neto Joana P. , Atallah Bassam V. , Soares Sofia , Moreira Luís , Matias Sara , Itskov Pavel M. , Correia Patrícia A. , Medina Roberto E. , Calcaterra Lorenza , Dreosti Elena , Paton Joseph J. , Kampff Adam R. 
Published: July 2014

AbstractThe design of modern scientific experiments requires the control and monitoring of many parallel data streams. However, the serial execution of programming instructions in a computer makes it a challenge to develop software that can deal with the asynchronous, parallel nature of scientific data. Here we present Bonsai, a modular, high-performance, open-source visual programming framework for the acquisition and online processing of data streams. We describe Bonsai’s core principles and architecture and demonstrate how it allows for flexible and rapid prototyping of integrated experimental designs in neuroscience. We specifically highlight different possible applications which require the combination of many different hardware and software components, i0ncluding behaviour video tracking, electrophysiology and closed-loop control of stimulation parameters.