bluuebunny/crossref_metadata_2025_split huggingface dataset:
Solution NMR characterization of WTCXCL8 monomer and dimer binding to CXCR1 N‐terminal domain
Authors: Joseph Prem Raj B. , Rajarathnam Krishna 
Published: October 2014

AbstractChemokine CXCL8 and its receptor CXCR1 are key mediators in combating infection and have also been implicated in the pathophysiology of various diseases including chronic obstructive pulmonary disease (COPD) and cancer. CXCL8 exists as monomers and dimers but monomer alone binds CXCR1 with high affinity. CXCL8 function involves binding two distinct CXCR1 sites – the N‐terminal domain (Site‐I) and the extracellular/transmembrane domain (Site‐II). Therefore, higher monomer affinity could be due to stronger binding at Site‐I or Site‐II or both. We have now characterized the binding of a human CXCR1 N‐terminal domain peptide (hCXCR1Ndp) to WT CXCL8 under conditions where it exists as both monomers and dimers. We show that the WT monomer binds the CXCR1 N‐domain with much higher affinity and that binding is coupled to dimer dissociation. We also characterized the binding of two CXCL8 monomer variants and a trapped dimer to two different hCXCR1Ndp constructs, and observe that the monomer binds with ∼10‐ to 100‐fold higher affinity than the dimer. Our studies also show that the binding constants of monomer and dimer to the receptor peptides, and the dimer dissociation constant, can vary significantly as a function of pH and buffer, and so the ability to observe WT monomer peaks is critically dependent on NMR experimental conditions. We conclude that the monomer is the high affinity CXCR1 agonist, that Site‐I interactions play a dominant role in determining monomer vs. dimer affinity, and that the dimer plays an indirect role in regulating monomer function.
Irreversible electroporation: Just another form of thermal therapy?
Authors: van Gemert Martin J. C. , Wagstaff Peter G. K. , de Bruin Daniel M. , van Leeuwen Ton G. , van der Wal Allard C. , Heger Michal , van der Geld Cees W. M. 
Published: October 2014

BACKGROUNDIrreversible electroporation (IRE) is (virtually) always called non‐thermal despite many reports showing that significant Joule heating occurs. Our first aim is to validate with mathematical simulations that IRE as currently practiced has a non‐negligible thermal response. Our second aim is to present a method that allows simple temperature estimation to aid IRE treatment planning.METHODSWe derived an approximate analytical solution of the bio‐heat equation for multiple 2‐needle IRE pulses in an electrically conducting medium, with and without a blood vessel, and incorporated published observations that an electric pulse increases the medium's electric conductance.RESULTSIRE simulation in prostate‐resembling tissue shows thermal lesions with 67–92°C temperatures, which match the positions of the coagulative necrotic lesions seen in an experimental study. Simulation of IRE around a blood vessel when blood flow removes the heated blood between pulses confirms clinical observations that the perivascular tissue is thermally injured without affecting vascular patency.CONCLUSIONSThe demonstration that significant Joule heating surrounds current multiple‐pulsed IRE practice may contribute to future in‐depth discussions on this thermal issue. This is an important subject because it has long been under‐exposed in literature. Its awareness pleads for preventing IRE from calling “non‐thermal” in future publications, in order to provide IRE‐users with the most accurate information possible. The prospect of thermal treatment planning as outlined in this paper likely aids to the important further successful dissemination of IRE in interventional medicine. Prostate 75:332–335, 2015. © 2014 The Authors. The Prostate Published by Wiley Periodicals, Inc.
Efficacy studies of an antibody‐drug conjugate PSMA‐ADC in patient‐derived prostate cancer xenografts
Authors: DiPippo Vincent A. , Olson William C. , Nguyen Holly M. , Brown Lisha G. , Vessella Robert L. , Corey Eva 
Published: October 2014

BACKGROUNDIt is timely and important to develop new treatment modalities for advanced prostate cancer, because even the newly FDA approved treatments, despite providing significant survival benefits, do not constitute cure of this disease. Antibody drug conjugates (ADCs) represent a promising approach to cancer therapy. Prostate‐specific membrane antigen (PSMA) is expressed in advanced prostate cancer and targeting this protein is used for imaging of advanced prostate cancer as well as development of targeting strategies. The objective of our studies was to evaluate the efficacy of PSMA ADC against a series of patient‐derived prostate cancer xenografts (LuCaP 58, LuCaP 77, LuCaP 96CR, and LuCaP 105) with different characteristics, including varying levels of PSMA expression and responses to androgen suppression.METHODSMice bearing subcutaneous LuCaP prostate cancer‐derived xenografts received PSMA antibody monomethyl auristatin E (MMAE) drug conjugate (PSMA ADC) in which the antibody and MMAE are linked via a protease‐cleavable linker. PSMA ADC dose ranged from 1 to 6 mg/kg. Unmodified PSMA mAb + free MMAE at the amount equivalent to those contained in 6 mg/kg PSMA ADC was used as control. All treatments were administered once a week via tail‐vein injections and repeated four times once a week and tumor responses were monitored for 10 weeks. IHC analyses were performed to determine PSMA and AR expression and effects on proliferation.RESULTSTreatment responses varied widely across the tumor models, from complete tumor regressions in LuCaP 96CR to largely unimpeded tumor progression of LuCaP 58, which had the lowest baseline level of PSMA expression. Intermediate antitumor effects were seen for LuCaP 77 and LuCaP 105 tumors, despite their having similar basal expression of PSMA as LuCaP 96CR. Interestingly, we detected substantial differences in responses even within the same model, indicating that PSMA expression is not the only factor involved in treatment outcomes.CONCLUSIONSOur results show high efficacy of PSMA ADC in advanced prostate cancer but also considerable variability in effects despite PSMA expression. Further studies to identify tumor characteristics that are predictive of treatment response are ongoing. Prostate 75:303–313, 2015. © 2014 Wiley Periodicals, Inc.
Can erbium dopant occupy both cation sites in cubic barium titanate via a mechanism different than self‐compensation?
Authors: Zulueta Y. A. , Guerrero F. , Leyet Y. , Anglada‐Rivera J. , González‐Romero R. L. , Meléndez Juan J. 
Published: October 2014

The defect energetics for several dopant incorporation modes and the dielectric–electric properties in Er‐doped BaTiO3 were studied by numerical simulations and the dielectric modulus formalism. Two “mixed” incorporation modes, both compatible with the existence of oxygen vacancies, are proposed. Simulation results for the solution energies show that, despite self‐compensation is the most favourable mode, the mixed modes exhibit quite similar energies and, therefore, could be active under some conditions. The incorporation of Er3+ into the BaTiO3 lattice decreases the dc conductivities with respect to the undoped case at high temperatures. Molecular Dynamics calculations and experimental measurements about conducting properties of Er‐doped BaTiO3 allow one to calculate activation energies for ionic conductivity, which agree with data for oxygen migration. Experimental and Molecular Dynamics data are then correlated with the possible defect configurations. Scheme of the defect clusters corresponding to the proposed mixed incorporation mechanisms: (a) “Ti‐vac” and (b) “Ba‐vac”. Green, grey, blue, and red balls correspond, respectively, to Ba2+, Ti4+, Er3+, and O2− ions.
Computation of the real structured singular value via pole migration
Authors: Iordanov P. , Halton M. 
Published: October 2014

SummaryThe paper introduces a new computationally efficient algorithm to determine a lower bound on the real structured singular value μ. The algorithm is based on a pole migration approach where an optimization solver is used to compute a lower bound on real μ independent of a frequency sweep. A distinguishing feature of this algorithm from other frequency independent one‐shot tests is that multiple localized optima (if they exist) are identified and returned from the search. This is achieved by using a number of alternative methods to generate different initial conditions from which the optimization solver can initiate its search from. The pole migration algorithm presented has also been extended to determine lower bounds for complex parametric uncertainties as well as full complex blocks. However, the results presented are for strictly real and repeated parametric uncertainty problems as this class of problem is the focus of this paper and are in general the most difficult to solve. Copyright © 2014 John Wiley & Sons, Ltd.
Wind field simulation and wind‐induced responses of large wind turbine tower‐blade coupled structure
Authors: Ke S T , Ge Y J , Wang T G , Cao J F , Tamura Y 
Published: October 2014

SummaryHerein, by a case study on a 5‐MW wind turbine system developed by Nanjing University of Aeronautics and Astronautics, the wind field simulation and wind‐induced vibration characteristics of wind turbine tower‐blade coupled systems is analyzed. First, the blade‐nacelle‐tower‐basis integrated finite element model with centrifugal forces induced by rotational blades is established. Then, based on a harmony superposition method and the modified blade element‐momentum theory, the fluctuating wind field of tower‐blade coupled systems is simulated, which considers wind shear effect, tower shadow effect, rotational effect, blade‐tower dynamic and model interaction effects. Finally, the wind‐induced dynamic responses and wind vibration coefficients of the wind turbine tower‐blade coupled structure are discussed through the ‘consistent coupled method’ previously proposed by us. The results indicate that the wind‐induced responses of a large wind turbine tower‐blade coupled structure present complicated modal responses and multimode coupling effect. Additionally, the rotational effect would amplify aerodynamic loads on blades with high frequency, wind‐induced dynamic responses and wind vibration coefficients of wind turbine tower. The centrifugal force effect could also amplify natural vibration frequency of the tower‐blade coupled system and reduce the wind‐induced dynamic responses and wind vibration coefficients of wind turbine tower. The research could contribute to wind‐resistant design of structure for a large‐scale wind turbine tower‐blade system. Copyright © 2014 John Wiley & Sons, Ltd.
Processing of preribosomal RNA in Saccharomyces cerevisiae
Authors: Fernández‐Pevida Antonio , Kressler Dieter , de la Cruz Jesús 
Published: October 2014

Most, if not all RNAs, are transcribed as precursors that require processing to gain functionality. Ribosomal RNAs (rRNA) from all organisms undergo both exo‐ and endonucleolytic processing. Also, in all organisms, rRNA processing occurs inside large preribosomal particles and is coupled to nucleotide modification, folding of the precursor rRNA (pre‐rRNA), and assembly of the ribosomal proteins (r‐proteins). In this review, we focus on the processing pathway of pre‐rRNAs of cytoplasmic ribosomes in the yeast Saccharomyces cerevisiae, without doubt, the organism where this pathway is best characterized. We summarize the current understanding of the rRNA maturation process, particularly focusing on the pre‐rRNA processing sites, the enzymes responsible for the cleavage or trimming reactions and the different mechanisms that monitor and regulate the pathway. Strikingly, the overall order of the various processing steps is reasonably well conserved in eukaryotes, perhaps reflecting common principles for orchestrating the concomitant events of pre‐rRNA processing and ribosome assembly. WIREs RNA 2015, 6:191–209. doi: 10.1002/wrna.1267This article is categorized under:

RNA Interactions with Proteins and Other Molecules > RNA–Protein Complexes
Translation > Ribosome Biogenesis
RNA Processing > rRNA Processing
Ilf3 and NF90 functions in RNA biology
Authors: Castella Sandrine , Bernard Rozenn , Corno Mélanie , Fradin Aurélie , Larcher Jean‐Christophe 
Published: October 2014

Double‐stranded RNA‐binding proteins (DRBPs) are known to regulate many processes of RNA metabolism due, among others, to the presence of double‐stranded RNA (dsRNA)‐binding motifs (dsRBMs). Among these DRBPs, Interleukin enhancer‐binding factor 3 (Ilf3) and Nuclear Factor 90 (NF90) are two ubiquitous proteins generated by mutually exclusive and alternative splicings of the Ilf3 gene. They share common N‐terminal and central sequences but display specific C‐terminal regions. They present a large heterogeneity generated by several post‐transcriptional and post‐translational modifications involved in their subcellular localization and biological functions. While Ilf3 and NF90 were first identified as activators of gene expression, they are also implicated in cellular processes unrelated to RNA metabolism such as regulation of the cell cycle or of enzymatic activites. The implication of Ilf3 and NF90 in RNA biology will be discussed with a focus on eukaryote transcription and translation regulation, on viral replication and translation as well as on noncoding RNA field. WIREs RNA 2015, 6:243–256. doi: 10.1002/wrna.1270This article is categorized under:

RNA Interactions with Proteins and Other Molecules > Protein–RNA Recognition
RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications
The role of social comparison for maximizers and satisficers: Wanting the best or wanting to be the best?
Authors: Weaver Kimberlee , Daniloski Kim , Schwarz Norbert , Cottone Keenan 
Published: October 2014

AbstractConsumers chose between options that paired either an objectively inferior good with high relative standing (Your laptop is rated 60/100 in quality; others' laptops are rated 50/100) or an objectively superior good with low relative standing (Your laptop is rated 80/100 in quality; others' laptops are rated 95/100). Decision makers who try to make the “best” decision, known as maximizers (Schwartz et al., 2002), pursued relative standing more than decision makers who are satisfied with outcomes that are “good enough” (known as satisficers). That is, maximizers were more likely than satisficers to choose objectively inferior products when they were associated with higher relative standing. Subsequent analyses investigating decisions across time showed that maximizers' interest in relative standing persisted even when the nature of the tradeoff was made overt, suggesting it is a conscious aspect of the maximizer identity. Overall, results suggest that the maximizer self concept is more complex than has been previously assumed—they are focused on relative outcomes in addition to absolute outcomes.
Wahrgenommene Verfügbarkeit und Alkoholkonsum Jugendlicher im Längsschnitt
Authors: Suchert Vivien , Hanewinkel Reiner , Morgenstern Matthis 
Published: October 2014

Zielsetzung: Untersuchung des Einflusses der wahrgenommenen Verfügbarkeit von Alkohol auf die Initiierung des Rauschtrinkens im Kindes- und Jugendalter Methodik: Es handelt sich um eine längsschnittliche Beobachtungsstudie mit drei Erhebungszeitpunkten über einen Zeitraum von 30 Monaten. Die Daten wurden an 1167 Schüler/innen mittels Fragebögen erhoben. Ergebnisse: Die Wahrscheinlichkeit für die Initiierung des Rauschtrinkens im Beobachtungszeitraum war bei Kindern und Jugendliche, die die Verfügbarkeit von Bier/Wein als hoch einschätzten, im Vergleich zu denen, die sie für gering erachteten, mit einem Chancenverhältnis (Adjustiertes Odds Ratio: AOR) von 1,54 (95 % Konfidenzintervall (KI): 1,14 – 2,09; p = 0,005) signifikant erhöht. Auch die wahrgenommene Verfügbarkeit von Spirituosen stellte sich als signifikanter Prädiktor heraus (AOR = 1,59; 95 % KI: 1,10 – 2,32; p = 0,014). Hier ergab sich weiterhin ein signifikanter Interaktionseffekt mit dem Alter der Kinder und Jugendlichen (AOR = 3,01; 95 % KI: 1,35 – 6,74; p = 0,007). Ein signifikanter Einfluss der wahrgenommenen Verfügbarkeit von Spirituosen konnte lediglich bei älteren Jugendlichen gefunden werden. Schlussfolgerungen: Neben politischen Maßnahmen zur Regulation der objektiven Verfügbarkeit von Alkohol (Mindestbezugsalter, Öffnungszeiten und Dichte von Verkaufsstellen) erscheint im Hinblick auf die subjektive Verfügbarkeit auch die Berücksichtigung des unmittelbaren sozialen Umfeldes für präventive Maßnahmen von Bedeutung zu sein.
Impact of Verb Tense on Response to the Four-Dimensional Symptom	Questionnaire (4DSQ)
Authors: Terluin Berend , Marchand Miquelle A. G. , de Vet Henrica C. W. , Brouwers Evelien P. M. 
Published: October 2014

Abstract. The verb tense of a questionnaire hypothetically might influence the way people respond to its items. We examined the effects of the verb tense on the response to the Four-Dimensional Symptom Questionnaire (4DSQ) in a population-based sample (N = 4,959; present tense N = 605; past tense N = 4,354). We determined whether the verb tense impacted the overall response rate, the scale structure, differential item functioning, reliability, proportions of respondents scoring above a range of cut-offs, and mean scale scores. The verb tense did not influence response rate, scale structure, item functioning, and reliability. The present tense increased the number of respondents scoring above very low cut-offs for distress and somatization. The effect on mean scale scores was limited and of little clinical importance.
Helicity conservation by flow across scales in reconnecting vortex links and knots
Authors: Scheeler Martin W. , Kleckner Dustin , Proment Davide , Kindlmann Gordon L. , Irvine William T. M. 
Published: October 2014

Significance
Ideal fluids have a conserved quantity—helicity—which measures the degree to which a fluid flow is knotted and tangled. In real fluids (even superfluids), vortex reconnection events disentangle linked and knotted vortices, jeopardizing helicity conservation. By generating vortex trefoil knots and linked rings in water and simulated superfluids, we observe that helicity is remarkably conserved despite reconnections: vortex knots untie and links disconnect, but in the process they create helix-like coils with the same total helicity. This result establishes helicity as a fundamental building block, like energy or momentum, for understanding the behavior of complex knotted structures in physical fields, including plasmas, superfluids, and turbulent flows.
Protein kinase IKKβ-catalyzed phosphorylation of IRF5 at Ser462 induces its dimerization and nuclear translocation in myeloid cells
Authors: Lopez-Pelaez Marta , Lamont Douglas J. , Peggie Mark , Shpiro Natalia , Gray Nathanael S. , Cohen Philip 
Published: October 2014

Significance
NF-κB and IFN Regulatory Factor 5 (IRF5) are required for the transcription of many proinflammatory cytokines in myeloid cells. The protein kinase IKKβ is the major activator of NF-κB but how IRF5 is activated has been unclear. This paper demonstrates that IKKβ also activates IRF5 by catalyzing the phosphorylation of Ser462. The phosphorylation of this serine induces the dimerization of IRF5 and its translocation to the nucleus. The activation of the master transcription factors of the innate immune system by the same protein kinase provides a mechanism for the coordinated control of IRF5 and NF-κB in response to inflammatory stimuli.
Copula‐Based Models of Systemic Risk in U.S. Agriculture: Implications for Crop Insurance and Reinsurance Contracts
Authors: Goodwin Barry K. , Hungerford Ashley 
Published: October 2014

AbstractThe federal crop insurance program has been a major fixture of U.S. agricultural policy since the 1930s, and continues to grow in size and importance. Indeed, it now represents the most prominent farm policy instrument, accounting for more government spending than any other farm commodity program. The 2014 Farm Bill further expanded the crop insurance program and introduced a number of new county‐level revenue insurance plans. In 2013, over $123 billion in crop value was insured under the program. Crop revenue insurance, first introduced in the 1990s, now accounts for nearly 70% of the total liability in the program. The available plans cover losses that result from a revenue shortfall that can be triggered by multiple, dependent sources of risk—either low prices, low yields, or a combination of both. The actuarial practices currently applied when rating these plans essentially involve the application of a Gaussian copula model to the pricing of dependent risks. We evaluate the suitability of this assumption by considering a number of alternative copula models. In particular, we use combinations of pair‐wise copulas of conditional distributions to model multiple sources of risk. We find that this approach is generally preferred by model‐fitting criteria in the applications considered here. We demonstrate that alternative approaches to modeling dependencies in a portfolio of risks may have significant implications for premium rates in crop insurance.
piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing
Authors: Han Bo W. , Wang Wei , Zamore Phillip D. , Weng Zhiping 
Published: October 2014

Motivation: PIWI-interacting RNAs (piRNAs), 23–36 nt small silencing RNAs, repress transposon expression in the metazoan germ line, thereby protecting the genome. Although high-throughput sequencing has made it possible to examine the genome and transcriptome at unprecedented resolution, extracting useful information from gigabytes of sequencing data still requires substantial computational skills. Additionally, researchers may analyze and interpret the same data differently, generating results that are difficult to reconcile. To address these issues, we developed a coordinated set of pipelines, ‘piPipes’, to analyze piRNA and transposon-derived RNAs from a variety of high-throughput sequencing libraries, including small RNA, RNA, degradome or 7-methyl guanosine cap analysis of gene expression (CAGE), chromatin immunoprecipitation (ChIP) and genomic DNA-seq. piPipes can also produce figures and tables suitable for publication. By facilitating data analysis, piPipes provides an opportunity to standardize computational methods in the piRNA field.
Supplementary information: Supplementary information, including flowcharts and example figures for each pipeline, are available at Bioinformatics online.
Availability and implementation: piPipes is implemented in Bash, C++, Python, Perl and R. piPipes is free, open-source software distributed under the GPLv3 license and is available at http://bowhan.github.io/piPipes/.
Contact: Phillip.Zamore@umassmed.edu or Zhiping.Weng@umassmed.edu
Supplementary information: Supplementary Data are available at Bioinformatics online.
SYSBIONS: nested sampling for systems biology
Authors: Johnson Rob , Kirk Paul , Stumpf Michael P. H. 
Published: October 2014

Motivation: Model selection is a fundamental part of the scientific process in systems biology. Given a set of competing hypotheses, we routinely wish to choose the one that best explains the observed data. In the Bayesian framework, models are compared via Bayes factors (the ratio of evidences), where a model’s evidence is the support given to the model by the data. A parallel interest is inferring the distribution of the parameters that define a model. Nested sampling is a method for the computation of a model’s evidence and the generation of samples from the posterior parameter distribution.Results: We present a C-based, GPU-accelerated implementation of nested sampling that is designed for biological applications. The algorithm follows a standard routine with optional extensions and additional features. We provide a number of methods for sampling from the prior subject to a likelihood constraint.Availability and implementation: The software SYSBIONS is available from http://www.theosysbio.bio.ic.ac.uk/resources/sysbions/Contact: m.stumpf@imperial.ac.uk, robert.johnson11@imperial.ac.uk