bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anaesthetic and post-operative management of a modified Norwood operation for hypoplastic left heart syndrome: a retrospective series of 11 cases
Authors: Yildiz Yahya , Kirbas Ahmet , Gurer Onur , S. Bilal Mehmet 
Published: February 2011

AbstractObjectiveThis study aimed to describe the pre-operative and operative findings, as well as the post-operative haemodynamics of patients operated on for hypoplastic left heart. The findings of patients who survived or did not survive were also compared to anticipate the risk factors for mortality.MethodsWe retrospectively reviewed the anaesthetic and intensive care records of 11 (seven male and four female) patients who underwent a modified Norwood operation as neonates. There were eight patients who survived, while three did not survive after the operation. Haemodynamics, oxygenation, and medications of patients were recorded for the pre-operative and post-operative conditions for 2 days, and compared between groups of patients who survived and those who did not.ResultsThe normalised modified Blalock–Taussig shunt area was 3.28, 0.57 square millimetres per kilogram (mean, standard deviation) for the group of patients who survived and 3.55, 1.4 square millimetres per kilogram for the group of patients who did not survive (p = 0.51). The group of patients who survived had a significantly larger normalised aortic annulus area (3.3, 0.89 square millimetres per kilogram versus 1.68, 0.21 square millimetres per kilogram, p = 0.01), lower median age (5.57 (3–8) days versus 46.67 (4–90) days, p = 0.02), and lower weight (2.95, 0.46 kilograms versus 3.85, 0.56 kilograms, p = 0.03) than the group of patients who did not survive. Furthermore, the group of patients who did not survive had a significantly worse pre-operative condition, lower systemic venous and arterial oxygen saturation, and need for a high dose of drugs in the pre-operative and post-operative periods (p was less than 0.05 for each variable).ConclusionThe pre-operative, operative, and post-operative findings may be related to mortality early after the modified Norwood operation for hypoplastic left heart syndrome.
Early extubation in tetralogy of Fallot patients after complete repair
Authors: Karthekeyan Ranjith Baskar , Sundar Ayya Syama , Sulaiman Sajith , Thangavelu Periyasamy , Vakamudi Mahesh , Kasianandan Thenali 
Published: February 2011

AbstractAimTo document the feasibility of early extubation and to know the effect of age, weight, and post-operative right ventricle/left ventricle ratio in early extubation in intracardiac repair for tetralogy of Fallot.Materials and methodsThis is a prospective study of 76 consecutive patients undergoing intracardiac repair between January, 2010 and April, 2010. The patients were compared between duration of ventilation with age, weight, and post-operative left ventricle/right ventricle ratio.ResultsIn the age group less than 10 years, 47 patients were extubated within 4 hours and 12 after 4 hours. In the age group of 10–20 years, eight patients were extubated within 4 hours and seven patients after 4 hours. In the more than 20 years category, one patient was extubated within 4 hours and the other after 4 hours. In the weight category less than 10 kilograms, 17 patients were extubated within 4 hours and seven patients after 4 hours. In the 10–20 kilogram category, 27 patients were extubated before 4 hours and four patients after 4 hours. In the more than 20-kilogram category, 12 patients were extubated before 4 hours and nine patients after 4 hours. Where the ratio was less than 0.5, 47 patients were extubated within 4 hours and 14 patients after 4 hours. Where the ratio was greater than 0.5, nine patients were extubated within 4 hours and six patients after 4 hours.ConclusionThere was no correlation between duration of ventilation with age, weight, and right ventricle/left ventricle ratio. Early extubation in patients after intracardiac repair in tetralogy of Fallot is safe and effective.
Institutions and development: generalizations that endanger progress
Authors: NUGENT JEFFREY B. 
Published: February 2011

Abstract:This article draws on several of the major breakthroughs in the institutions and development field to demonstrate that criticisms of work in this field as a whole based on its allegedly universal and unquestioning support for liberalizing institutions and the simplistic rationale and deficient empirical methods that have been used to buttress that support are outdated, inappropriate and misleading.
The International Committee of the Red Cross in Afghanistan: reasserting the neutrality of humanitarian action
Authors: Terry Fiona 
Published: February 2011

AbstractNeutrality as a guiding principle of humanitarian action was roundly rejected by most actors in Afghanistan's latest conflict. One party to the conflict commandeered assistance and aid organizations into a counter-insurgency campaign, and the other rejected Western aid organizations as agents of an imperialist West. The murder in 2003 of the International Committee of the Red Cross (ICRC) water engineer Ricardo Munguia, because of what he symbolized, cast doubt on whether the ICRC could be perceived as neutral in this highly polarized context. Rather than abandon a neutral stance, however, as so many aid organizations did, the ICRC persevered and, through some innovative and sometimes risky initiatives, managed to show both sides the benefits of having a neutral intermediary in conflict. Today, the ICRC continues to expand its reach to Afghans in dire need of humanitarian assistance.
Quantum chemical assessment of the binding energy of CuO+
Authors: Rezabal Elixabete , Gauss Jürgen , Matxain Jon M. , Berger Robert , Diefenbach Martin , Holthausen Max C. 
Published: February 2011

We present a detailed theoretical investigation on the dissociation energy of CuO+, carried out by means of coupled cluster theory, the multireference averaged coupled pair functional (MR-ACPF) approach, diffusion quantum Monte Carlo (DMC), and density functional theory (DFT). At the respective extrapolated basis set limits, most post-Hartree–Fock approaches agree within a narrow error margin on a De value of 26.0 kcal mol−1 [coupled-cluster singles and doubles level augmented by perturbative triples corrections, CCSD(T)], 25.8 kcal mol−1 (CCSDTQ via the high accuracy extrapolated ab initio thermochemistry protocol), and 25.6 kcal mol−1 (DMC), which is encouraging in view of the disaccording data published thus far. The configuration-interaction based MR-ACPF expansion, which includes single and double excitations only, gives a slightly lower value of 24.1 kcal mol−1, indicating that large basis sets and triple excitation patterns are necessary ingredients for a quantitative assessment. Our best estimate for D0 at the CCSD(T) level is 25.3 kcal mol−1, which is somewhat lower than the latest experimental value (D0 = 31.1 ± 2.8 kcal mol−1; reported by the Armentrout group) [Int. J. Mass Spectrom. 182/183, 99 (1999)]. These highly correlated methods are, however, computationally very demanding, and the results are therefore supplemented with those of more affordable DFT calculations. If used in combination with moderately-sized basis sets, the M05 and M06 hybrid functionals turn out to be promising candidates for studies on much larger systems containing a [CuO]+ core.
The C–H bond dissociation energy of furan: Photoelectron spectroscopy of the furanide anion
Authors: Vogelhuber Kristen M. , Wren Scott W. , Sheps Leonid , Lineberger W. Carl 
Published: February 2011

Using photoelectron spectroscopy, we interrogate the cyclic furanide anion (C4H3O−) to determine the electron affinity and vibrational structure of the neutral furanyl radical and the term energy of its first excited electronic state. We present the 364-nm photoelectron spectrum of the furanide anion and measure the electron affinity of the $\tilde X^2 {\rm A' }$X̃2A′ ground state of the α-furanyl radical to be 1.853(4) eV. A Franck–Condon analysis of the well-resolved spectrum allows determination of the harmonic frequencies of three of the most active vibrational modes upon $\tilde X^2 {\rm A' }$X̃2A′ ← $\tilde X^1 {\rm A' }$X̃1A′ photodetachment: 855(25), 1064(25), and 1307(40) cm−1. These modes are ring deformation vibrations, consistent with the intuitive picture of furanide anion photodetachment, where the excess electron is strongly localized on the α-carbon atom. In addition, the $\tilde A^2 {\rm A^{\prime \prime}}$Ã2A′′ excited state of the α-furanyl radical is observed 0.68(7) eV higher in energy than the $\tilde X^2 {\rm A' }$X̃2A′ ground state. Through a thermochemical cycle involving the known gas-phase acidity of furan, the electron affinity of the furanyl radical yields the first experimental determination of the C–Hα bond dissociation energy of furan (DH298(C4H3O–Hα)): 119.8(2) kcal mol−1.
Low-resolution structure of a vesicle disrupting α-synuclein oligomer that accumulates during fibrillation
Authors: Giehm Lise , Svergun Dmitri I. , Otzen Daniel E. , Vestergaard Bente 
Published: February 2011

One of the major hallmarks of Parkinson disease is aggregation of the protein α-synuclein (αSN). Aggregate cytotoxicity has been linked to an oligomeric species formed at early stages in the aggregation process. Here we follow the fibrillation process of αSN in solution over time using small angle X-ray scattering and resolve four major coexisting species in the fibrillation process, namely monomer, dimer, fibril and an oligomer. By ab initio modeling to fit the data, we obtain a low-resolution structure of a symmetrical and slender αSN fibril in solution, consisting of a repeating unit with a maximal distance of 900 Å and a diameter of ∼180
Å
. The same approach shows the oligomer to be shaped like a wreath, with a central channel and with dimensions corresponding to the width of the fibril. The structure, accumulation and decay of this oligomer is consistent with an on-pathway role for the oligomer in the fibrillation process. We propose an oligomer-driven αSN fibril formation mechanism, where the fibril is built from the oligomers. The wreath-shaped structure of the oligomer highlights its potential cytotoxicity by simple membrane permeabilization. This is confirmed by the ability of the purified oligomer to disrupt liposomes. Our results provide the first structural description in solution of a potentially cytotoxic oligomer, which accumulates during the fibrillation of αSN.
Phage display can select over-hydrophobic sequences that may impair prediction of natural domain–peptide interactions
Authors: Luck Katja , Travé Gilles 
Published: February 2011

Abstract
Motivation: The phage display peptide selection approach is widely used for defining binding specificities of globular domains. PDZ domains recognize partner proteins via C-terminal motifs and are often used as a model for interaction predictions. Here, we investigated to which extent phage display data that were recently published for 54 human PDZ domains can be applied to the prediction of human PDZ–peptide interactions.
Results: Promising predictions were obtained for one-third of the 54 PDZ domains. For the other two-thirds, we detected in the phage display peptides an important bias for hydrophobic amino acids that seemed to impair correct predictions. Therefore, phage display-selected peptides may be over-hydrophobic and of high affinity, while natural interaction motifs are rather hydrophilic and mostly combine low affinity with high specificity. We suggest that potential amino acid composition bias should systematically be investigated when applying phage display data to the prediction of specific natural domain–linear motif interactions.
Contact: katja.luck@unistra.fr; gilles.trave@unistra.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
HLA*IMP—an integrated framework for imputing classical HLA alleles from SNP genotypes
Authors: Dilthey Alexander T. , Moutsianas Loukas , Leslie Stephen , McVean Gil 
Published: February 2011

Abstract
Motivation: Genetic variation at classical HLA alleles influences many phenotypes, including susceptibility to autoimmune disease, resistance to pathogens and the risk of adverse drug reactions. However, classical HLA typing methods are often prohibitively expensive for large-scale studies. We previously described a method for imputing classical alleles from linked SNP genotype data. Here, we present a modification of the original algorithm implemented in a freely available software suite that combines local data preparation and QC with probabilistic imputation through a remote server.
Results: We introduce two modifications to the original algorithm. First, we present a novel SNP selection function that leads to pronounced increases (up by 40% in some scenarios) in call rate. Second, we develop a parallelized model building algorithm that allows us to process a reference set of over 2500 individuals. In a validation experiment, we show that our framework produces highly accurate HLA type imputations at class I and class II loci for independent datasets: at call rates of 95–99%, imputation accuracy is between 92% and 98% at the four-digit level and over 97% at the two-digit level. We demonstrate utility of the method through analysis of a genome-wide association study for psoriasis where there is a known classical HLA risk allele (HLA-C*06:02). We show that the imputed allele shows stronger association with disease than any single SNP within the region. The imputation framework, HLA*IMP, provides a powerful tool for dissecting the architecture of genetic risk within the HLA.
Availability: HLA*IMP, implemented in C++ and Perl, is available from http://oxfordhla.well.ox.ac.uk and is free for academic use.
Contact: mcvean@stats.ox.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
BioGRID REST Service, BiogridPlugin2 and BioGRID WebGraph: new tools for access to interaction data at BioGRID
Authors: Winter Andrew G. , Wildenhain Jan , Tyers Mike 
Published: February 2011

Abstract
Summary: The Biological General Repository for Interaction Datasets (BioGRID) representational state transfer (REST) service allows full URL-based access to curated protein and genetic interaction data at the BioGRID database. Appending URL parameters allows filtering of data by various attributes including gene names and identifiers, PubMed ID and evidence type. We also describe two visualization tools that interface with the REST service, the BiogridPlugin2 for Cytoscape and the BioGRID WebGraph.
Availability and implementation: BioGRID data and applications are completely free for commercial and non-commercial use. http://webservice.thebiogrid.org/resources/interactions (REST Service), http://wiki.thebiogrid.org/doku.php/biogridrest(REST Service parameter list and help), http://webservice.thebiogrid.org/resources/application.wadl(REST Service WADL), http://thebiogrid.org/download.php (BiogridPlugin2, v2.1 download), http://wiki.thebiogrid.org/doku.php/biogridplugin2 (BiogridPlugin2 help) and http://tyerslab.bio.ed.ac.uk/tools/BioGRID_webgraph.php(BioGRID WebGraph).
Contact: andrew.winter@ed.ac.uk, m.tyers@ed.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
uMELT: prediction of high-resolution melting curves and dynamic melting profiles of PCR products in a rich web application
Authors: Dwight Zachary , Palais Robert , Wittwer Carl T. 
Published: February 2011

Abstract
Summary: uMeltSM is a flexible web-based tool for predicting DNA melting curves and denaturation profiles of PCR products. The user defines an amplicon sequence and chooses a set of thermodynamic and experimental parameters that include nearest neighbor stacking energies, loop entropy effects, cation (monovalent and Mg++) concentrations and a temperature range. Using an accelerated partition function algorithm along with chosen parameter values, uMelt interactively calculates and visualizes the mean helicity and the dissociation probability at each sequence position at temperatures within the temperature range. Predicted curves display the mean helicity as a function of temperature or as derivative plots. Predicted profiles display stability as a function of sequence position either as 50% helicity temperatures or as the helicity probability at specific temperatures. The loss of helicity associated with increasing temperature may be viewed dynamically to visualize domain formation within the molecule. Results from fluorescent high-resolution melting experiments match the number of predicted melting domains and their relative temperatures. However, the absolute melting temperatures vary with the selected thermodynamic parameters and current libraries do not account for the rapid melting rates and helix stabilizing dyes used in fluorescent melting experiments. uMelt provides a convenient platform for simulation and design of high-resolution melting assays.
Availability and implementation: The application was developed in Actionscript and can be found online at http://www.dna.utah.edu/umelt/umelt.html. Adobe Flash is required to run in all browsers.
Contact: zach.dwight@path.utah.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Partners in Time: EARLY BIRD Associates with ZEITLUPE and Regulates the Speed of the Arabidopsis Clock
Authors: Johansson Mikael , McWatters Harriet G. , Bakó László , Takata Naoki , Gyula Péter , Hall Anthony , Somers David E. , Millar Andrew J. , Eriksson Maria E. 
Published: February 2011

Abstract
The circadian clock of the model plant Arabidopsis (Arabidopsis thaliana) is made up of a complex series of interacting feedback loops whereby proteins regulate their own expression across day and night. early bird (ebi) is a circadian mutation that causes the clock to speed up: ebi plants have short circadian periods, early phase of clock gene expression, and are early flowering. We show that EBI associates with ZEITLUPE (ZTL), known to act in the plant clock as a posttranslational mediator of protein degradation. However, EBI is not degraded by its interaction with ZTL. Instead, ZTL counteracts the effect of EBI during the day and increases it at night, modulating the expression of key circadian components. The partnership of EBI with ZTL reveals a novel mechanism involved in controlling the complex transcription-translation feedback loops of the clock. This work highlights the importance of cross talk between the ubiquitination pathway and transcriptional control for regulation of the plant clock.
Paediatric parenting stress in inflammatory bowel disease: application of the Pediatric Inventory for Parents
Authors: Guilfoyle S. M. , Denson L. A. , Baldassano R. N. , Hommel K. A. 
Published: February 2011

AbstractBackground  The psychosocial functioning of caregivers of adolescents managing inflammatory bowel disease (IBD) has been understudied; yet, poor caregiver functioning can place youth at risk for compromised disease management. The current study addressed this limitation by examining a sample of caregivers of adolescents with IBD. Study aims included (1) documenting rates of paediatric parenting stress; (2) identifying associated sociodemographic predictors of parenting stress; and (3) comparing previously published rates of parenting stress to those within other paediatric chronic conditions, including cancer, type 1 diabetes, obesity, sickle cell disease, bladder exstrophy.Methods  Caregivers of adolescents with an IBD diagnosis (Mage= 15.4 ± 1.4, 44.4% female, 88.7% Caucasian) and receiving tertiary care within a gastroenterology clinic (n= 62) completed the Pediatric Inventory for Parents (PIP) as a measure of paediatric parenting stress with frequency and difficulty as PIP subscales. Paediatric gastroenterologists provided disease severity assessments.Results  Adolescents with IBD were experiencing relatively mild disease activity. Bivariate correlations revealed that PIP‐difficulty was positively associated with Crohn's disease severity (r= 0.38, P < 0.01). Caregiver age was negatively associated with the frequency of parenting stress total (r=−0.25, P= 0.05) and communication scores (r=−0.25, P < 0.05). The frequency and difficulty of parenting stressors within the IBD sample were similar to rates within type 1 diabetes, but were significantly lower than rates identified in other paediatric chronic conditions.Conclusions  Caregivers of adolescents with IBD seem to experience low rates of parenting stress when their adolescents are receiving outpatient care and during phases of IBD relative inactivity. The sociodemographic characteristics of IBD families (i.e. primarily Caucasian, well‐educated and higher socio‐economic status) likely encourage greater access to financial and psychosocial resources, which may aid in promoting more optimal stress management.
Pharmacokinetics and pharmacodynamics of mycophenolate sodium (EC‐MPS) co‐administered with cyclosporine in the early‐phase post‐kidney transplantation
Authors: Stracke Sylvia , Shipkova Maria , Mayer Jens , Keller Frieder , Zarghom Amir , Yang Liying , Henne‐Bruns Doris , Wieland Eberhard 
Published: February 2011

Stracke S, Shipkova M, Mayer J, Keller F, Zarghom A, Yang L, Henne‐Bruns D, Wieland E. Pharmacokinetics and pharmacodynamics of mycophenolate sodium (EC‐MPS) co‐administered with cyclosporine in the early‐phase post‐kidney transplantation.  Clin Transplant 2012: 26: 57–66.  © 2011 John Wiley & Sons A/S.Abstract:  Mycophenolate drug levels are decreased by co‐administration of cyclosporine. However, mycophenolate levels may be associated with insufficient immunosuppression.We investigated the pharmacokinetics of 720 mg mycophenolate sodium (EC‐MPS) and inosine monophosphate dehydrogenase (IMPDH) activity under co‐medication with cyclosporine and steroids within the first 30 d after kidney transplantation (n = 24). Blood samples were drawn at 0, 0.5, 1, 1.5, 2, 3, 4, 6, 8, and 12 h after the morning dose. Plasma concentrations of mycophenolic acid, its glucuronide metabolites (MPAG; AcMPAG), and free MPA were determined using validated HPLC‐DAD. IMPDH activity in leukocytes was analyzed chromatographically.Only six of 24 patients had an MPA‐AUC12h within the putative therapeutic range of 40–60 mg/L·h. MPA clearance was high with 29 L/h. fMPA‐AUC12h (r = −0.429, p = 0.04) and MPAG‐AUC12h correlated significantly with the glomerular filtration rate, while total MPA did not. The MPAG‐AUC12h was about 52‐fold higher than the corresponding values for MPA, whereas the AcMPAG‐AUC12h reached about 20.4% of the respective MPA‐AUC12h. We found significant correlations between IMPDH inhibition and MPA concentration (r = −0.665; p < 0.0001), fMPA (r = −0.446; p = 0.003), and AcMPAG (r = −0.459; p = 0.002) but not with MPAG.Only 25% of the patients attained the therapeutic range for MPA‐AUC under standard EC‐MPS dose during the early‐phase post‐transplantation. We recommend that EC‐MPS should be given in higher doses (3 × 720 mg) in the early post‐transplant period when co‐administered with cyclosporine.