bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reticulocyte Hemoglobin Content During the First Month of Life in Critically Ill Very Low Birth Weight Neonates Differs From Term Infants, Children, and Adults
Authors: Al‐Ghananim Raeda T. , Nalbant Demet , Schmidt Robert L. , Cress Gretchen A. , Zimmerman M. Bridget , Widness John A. 
Published: May 2015

BackgroundReticulocyte hemoglobin content (RET‐He)—an established indicator of iron status in children and adults—was determined in very low birth weight (VLBW) infants.MethodsLongitudinal retrospective RET‐He data in 26 VLBW neonates during the first month of age were compared with: (a) concurrent complete blood counts (CBCs), including hemoglobin (Hb) concentration, reticulocyte count, and immature reticulocyte fraction (IRF), and erythropoietin (EPO) levels; (b) clinical variables; and (c) RET‐He data from the literature for term infants, children, and adults.ResultsRET‐He within 24 hr following birth was 31.8 ± 1.1 pg (mean ± SEM). This was followed by an abrupt, significant decline to 28.3 ± 1.1 pg at 2–4 days, and to steady state levels of 28.4 ± 0.5 pg thereafter. The changes in RET‐He were mirrored by changes in plasma EPO, reticulocyte count, and IRF, but not Hb. Steady state RET‐He values after 4 days were significantly lower than RET‐He values for term infants, children, and adults (31.6 ± 0.11, 32.0 ± 0.12, and 33.0 ± 0.13 pg, respectively).ConclusionAlthough RET‐He values in VLBW infant were lower than term infants, children, and adults, the significance and mechanism(s) responsible are unknown. The present VLBW infant data are relevant to investigations assessing hemoglobinization following treatment with recombinant human EPO (r‐HuEPO) and/or iron.
Evolution of viviparity in squamate reptiles: Reversibility reconsidered
Authors: Blackburn Daniel G. 
Published: May 2015

ABSTRACTViviparity in squamate reptiles is widely recognized as having evolved convergently from oviparity more than 100 times. However, questions persist as to whether reversals from viviparity back to oviparity have ever occurred. Based on a theoretical model, a recent paper (Pyron and Burbrink, 2014) has proposed that viviparity is ancestral for squamates and that viviparity—oviparity reversals have far outnumbered origins of viviparity in reproductive history. Close examination of this analysis reveals features that cast doubt on its plausibility, notably the requirement of repeated, sequential transformations back and forth between these reproductive modes, as well as numerous, uncounted evolutionary transformations that have produced inaccurate estimates of parsimony. Evidence derived from studies of anatomy, physiology, and developmental biology strongly supports the inference that oviparity is ancestral for squamates and has given rise to viviparity on numerous occasions. Biological data provide important insights into the likelihood of evolutionary transformations, and deserve to be incorporated fully into future analyses of the evolution of reproductive modes. J. Exp. Zool. (Mol. Dev. Evol.) 324B: 473–486, 2015. © 2015 Wiley Periodicals, Inc.
Numerical determination of coaxial cable parameters in cryogenic environments for high‐frequency active device noise modeling
Authors: Cleriti Riccardo , Colangeli Sergio , Ciccognani Walter , Palomba Mirko , Limiti Ernesto 
Published: May 2015

SummaryThis contribution presents an original mathematical method for numerically evaluating the noise parameters of a transmission line subject to an arbitrary thermal gradient. Compared with previous methods, this procedure permits to easily take into account possible variations of line parameters along the propagation direction due to very high thermal excursions. The principal application of the proposed method is coaxial cable modeling in noise figure measurement setups under cryogenic conditions: the connection cable or waveguide from the outside to the inside of the cryogenic vacuum chamber are subject to non‐negligible thermal excursions. Under these conditions, significant de‐embedding errors may arise if the cables are not correctly modeled, given the very low values of noise figure, which are commonly exhibited by in cryo‐cooled devices. The behavior of transmission lines subject to thermal gradients is investigated through extensive 3D thermal and electromagnetic simulations. Simulated data are then input to a numerical algorithm for efficiently determining both scattering and noise parameters of coaxial cables actually used in a cryogenic probe station developed and realized in the facilities of the University of Rome Tor Vergata. A measurement campaign has been performed to validate the simulation‐based approach. Subsequently, the numerical model has been used to de‐embed the noise contribution of the coaxial cables from cryogenic NF50 measurements of a 70 nm metamorphic high electron mobility transistor (mHEMT). Copyright © 2015 John Wiley & Sons, Ltd.
The uncertainty of break positions detected by homogenization algorithms in climate records
Authors: Lindau Ralf , Venema Victor 
Published: May 2015

ABSTRACTLong instrumental climate records suffer from inhomogeneities due to, e.g. relocations of the stations or changes in instrumentation, which may introduce sudden jumps into the time series. These inhomogeneities may mask or strengthen true trends. Relative homogenization algorithms use the difference time series of a candidate station with neighboring stations to identify such breaks (changepoints). Modern multiple breakpoint methods search for the optimum segmentation, which is characterized by minimum internal variance within the segments and maximum external variance between the segment means.We analyse the accuracy of these homogenization methods and concentrate on the uncertainty in the position of the break. Due to unavoidable random noise in the difference time series, the segmentation method may find a shifted break position, which attains a higher external variance than the true one. Different lengths of potentially exchanged subsegments are considered; that one providing the largest external variance will be chosen as possibly erroneous optimum. We will show that the variances of shifted segmentations can be approximated by a Brownian motion with drift, where the signal‐to‐noise ratio (SNR) defines the drift size.Available formulae for one‐sided and continuous Brownian motion with drift are expanded to two‐sided and discrete processes as they occur in praxis. The error probability increases strongly for SNRs lower than 1. Thus, when the internal variance is larger than the variance introduced by the breaks, the probability of finding the right break position is small.
Synoptic climatology of warm fronts in Southeastern South America
Authors: Ribeiro Bruno Zanetti , Seluchi Marcelo Enrique , Chou Sin Chan 
Published: May 2015

ABSTRACTThis study shows a synoptic climatology of warm fronts in Southeastern South America (SESA). Data from Climate Forecast System Reanalysis (CFSR) was used to identify warm fronts from 1979 to 2010. The identification method was based on the magnitude of meridional gradient of 850‐hPa equivalent potential temperature (θe) and 850‐hPa wind fields. Composites of the most important atmospheric variables were constructed from 1 day before until 1 day after the formation of the warm front. An average frequency of two warm fronts per month is observed, with higher frequencies in austral winter. Most warm fronts precede the formation of extratropical cyclones over Uruguay and form because of the southward movement of previous cold/stationary fronts. Warm fronts form on average around southern Paraguay, northeastern Argentina and western part of southern Brazil and Uruguay, coupled to the eastern edge of the Chaco Low (CL) and the Northwestern Argentinean Low (NAL) where north/northwesterly flow predominates. An upper‐level wave of wavenumber eight supports warm frontogenesis. Location and intensity of synoptic systems associated with a warm front event differ from winter to summer. Elevated instability is commonly present near warm fronts, and the average warm‐front slope is 1 : 110, agreeing with other studies. Instability indices increase after the warm‐front passage, leading to greater rainfall 1 day after the warm front forms.
Nanocomposite Foams of Polypropylene and Carbon Nanotubes: Preparation, Characterization, and Evaluation of their Performance as EMI Absorbers
Authors: Tran Minh‐Phuong , Thomassin Jean‐Michel , Alexandre Michaël , Jerome Christine , Huynen Isabelle , Detrembleur Christophe 
Published: May 2015

Highly expanded nanocomposite foams of polypropylene and carbon nanotubes (PP/CNT) are formed using supercritical carbon dioxide (scCO2) technology. The foaming parameters (temperature, pressure) are investigated to establish their influence on the morphology of the resulting foams and their impact on the electrical conductivity. As promising electromagnetic‐interference (EMI) absorbers, the EMI shielding performance of the foams is determined, and a preliminary relationship is established between foam morphology and the EMI shielding performance. The best candidates are highly expanded foams with a volume expansion of >25, containing 0.1 vol% CNTs; they are able to absorb more than 90% of the incident radiation between 25 and 40 GHz.
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An inexact shift‐and‐invert Arnoldi algorithm for Toeplitz matrix exponential
Authors: Wu Gang , Feng Ting‐ting , Wei Yimin 
Published: May 2015

SummaryWe revisit the shift‐and‐invert Arnoldi method proposed in [S. Lee, H. Pang, and H. Sun.Shift‐invert Arnoldi approximation to the Toeplitz matrix exponential, SIAM J. Sci. Comput., 32: 774–792, 2010] for numerical approximation to the product of Toeplitz matrix exponential with a vector. In this approach, one has to solve two large‐scale Toeplitz linear systems in advance. However, if the desired accuracy is high, the cost will be prohibitive. Therefore, it is interesting to investigate how to solve the Toeplitz systems inexactly in this method. The contribution of this paper is in three regards. First, we give a new stability analysis on the Gohberg–Semencul formula (GSF) and define the GSF condition number of a Toeplitz matrix. It is shown that when the size of the Toeplitz matrix is large, our result is sharper than the one given in [M. Gutknecht and M. Hochbruck.The stability of inversion formulas for Toeplitz matrices, Linear Algebra Appl., 223/224: 307–324, 1995]. Second, we establish a relation between the error of Toeplitz systems and the residual of Toeplitz matrix exponential. We show that if the GSF condition number of the Toeplitz matrix is medium‐sized, then the Toeplitz systems can be solved in a low accuracy. Third, based on this relationship, we present a practical stopping criterion for relaxing the accuracy of the Toeplitz systems and propose an inexact shift‐and‐invert Arnoldi algorithm for the Toeplitz matrix exponential problem. Numerical experiments illustrate the numerical behavior of the new algorithm and show the effectiveness of our theoretical results. Copyright © 2015 John Wiley & Sons, Ltd.
A prediction of dislocation‐free CdTe/CdS photovoltaic multilayers via nano‐patterning and composition grading
Authors: Zhou Xiao Wang , Ward Donald K. , Doty F. Patrick , Zimmerman Jonathan A. , Wong Bryan M. , Cruz‐Campa Jose Luis , Nielson Gregory N. , Chavez Jose Juan , Zubia David , McClure John C. 
Published: May 2015

AbstractDefects in multilayered films have long been a performance‐limiting problem for the semiconductor industry. For instance, CdTe/CdS solar cell efficiencies have had significant improvement in the past 15years or more without addressing the problem of high misfit dislocation densities. Overcoming this stagnation requires a fundamental understanding of interfacial defect formation. Herein, we demonstrate a new first principles‐based CdTe bond‐order approach that enables efficient molecular dynamics to approach the fidelity of density functional theory. Stringent quantum‐mechanical verification and experimental validation tests reveal that our new approach provides an accurate prediction of defects that earlier methods cannot. Using this new capability, we show that misfit dislocations in CdTe/CdS multilayers can be significantly reduced via nano‐patterning and composition grading and more importantly, dislocation‐free multilayers naturally arise when the pattern dimension is reduced below 90nm. Our predictive methods are generally applicable to other materials, highlighting a rational approach towards low‐defect semiconductor films. Copyright © 2015 John Wiley & Sons, Ltd.
Advanced analyses of kinetic stabilities of iggs modified by mutations and glycosylation
Authors: Sedlák Erik , Schaefer Jonas V. , Marek Jozef , Gimeson Peter , Plückthun Andreas 
Published: May 2015

AbstractThe stability of Immunoglobulin G (IgG) affects production, storage and usability, especially in the clinic. The complex thermal and isothermal transitions of IgGs, especially their irreversibilities, pose a challenge to the proper determination of parameters describing their thermodynamic and kinetic stability. Here, we present a reliable mathematical model to study the irreversible thermal denaturations of antibody variants. The model was applied to two unrelated IgGs and their variants with stabilizing mutations as well as corresponding non‐glycosylated forms of IgGs and Fab fragments. Thermal denaturations of IgGs were analyzed with three transitions, one reversible transition corresponding to CH2 domain unfolding followed by two consecutive irreversible transitions corresponding to Fab and CH3 domains, respectively. The parameters obtained allowed us to examine the effects of these mutations on the stabilities of individual domains within the full‐length IgG. We found that the kinetic stability of the individual Fab fragment is significantly lowered within the IgG context, possibly because of intramolecular aggregation upon heating, while the stabilizing mutations have an especially beneficial effect. Thermal denaturations of non‐glycosylated variants of IgG consist of more than three transitions and could not be analyzed by our model. However, isothermal denaturations demonstrated that the lack of glycosylation affects the stability of all and not just of the CH2 domain, suggesting that the partially unfolded domains may interact with each other during unfolding. Investigating thermal denaturation of IgGs according to our model provides a valuable tool for detecting subtle changes in thermodynamic and/or kinetic stabilities of individual domains.
Membrane proteins in their native habitat as seen by solid‐state NMR spectroscopy
Authors: Brown Leonid S. , Ladizhansky Vladimir 
Published: May 2015

AbstractMembrane proteins play many critical roles in cells, mediating flow of material and information across cell membranes. They have evolved to perform these functions in the environment of a cell membrane, whose physicochemical properties are often different from those of common cell membrane mimetics used for structure determination. As a result, membrane proteins are difficult to study by traditional methods of structural biology, and they are significantly underrepresented in the protein structure databank. Solid‐state Nuclear Magnetic Resonance (SSNMR) has long been considered as an attractive alternative because it allows for studies of membrane proteins in both native‐like membranes composed of synthetic lipids and in cell membranes. Over the past decade, SSNMR has been rapidly developing into a major structural method, and a growing number of membrane protein structures obtained by this technique highlights its potential. Here we discuss membrane protein sample requirements, review recent progress in SSNMR methodologies, and describe recent advances in characterizing membrane proteins in the environment of a cellular membrane.
A comparison of the folding characteristics of free and ribosome‐tethered polypeptide chains using limited proteolysis and mass spectrometry
Authors: Rajabi Khadijeh , Reuther Julia , Deuerling Elke , Radford Sheena E. , Ashcroft Alison E. 
Published: May 2015

AbstractThe kinetics and thermodynamics of protein folding are commonly studied in vitro by denaturing/renaturing intact protein sequences. How these folding mechanisms relate to de novo folding that occurs as the nascent polypeptide emerges from the ribosome is much less well understood. Here, we have employed limited proteolysis followed by mass spectrometry analyses to compare directly free and ribosome‐tethered polypeptide chains of the Src‐homology 3 (SH3) domain and its unfolded variant, SH3‐m10. The disordered variant was found to undergo faster proteolysis than SH3. Furthermore, the trypsin cleavage patterns observed show minor, but significant, differences for the free and ribosome‐bound nascent chains, with significantly fewer tryptic peptides detected in the presence of ribosome. The results highlight the utility of limited proteolysis coupled with mass spectrometry for the structural analysis of these complex systems, and pave the way for detailed future analyses by combining this technique with chemical labeling methods (for example, hydrogen‐deuterium exchange, photochemical oxidation) to analyze protein folding in real time, including in the presence of additional ribosome‐associated factors.
The role of conformational selection in the molecular recognition of the wild type and mutants XPA67‐80 peptides by ERCC1
Authors: Fadda Elisa 
Published: May 2015

ABSTRACTMolecular recognition is a fundamental step in the coordination of biomolecular pathways. Understanding how recognition and binding occur between highly flexible protein domains is a complex task. The conformational selection theory provides an elegant rationalization of the recognition mechanism, especially valid in cases when unstructured protein regions are involved. The recognition of a poorly structured peptide, namely XPA67‐80, by its target receptor ERCC1, falls in this challenging study category. The microsecond molecular dynamics (MD) simulations, discussed in this work, show that the conformational propensity of the wild type XPA67‐80 peptide in solution supports conformational selection as the key mechanism driving its molecular recognition by ERCC1. Moreover, all the mutations of the XPA67‐80 peptide studied here cause a significant increase of its conformational disorder, relative to the wild type. Comparison to experimental data suggests that the loss of the recognized structural motifs at the microscopic time scale can contribute to the critical decrease in binding observed for one of the mutants, further substantiating the key role of conformational selection in recognition. Ultimately, because of the high sequence identity and analogy in binding, it is conceivable that the conclusions of this study on the XPA67‐80 peptide also apply to the ERCC1‐binding domain of the XPA protein. Proteins 2015; 83:1341–1351. © 2015 Wiley Periodicals, Inc.
Rosetta comparative modeling for library design: Engineering alternative inducer specificity in a transcription factor
Authors: Jha Ramesh K. , Chakraborti Subhendu , Kern Theresa L. , Fox David T. , Strauss Charlie E. M. 
Published: May 2015

ABSTRACTStructure‐based rational mutagenesis for engineering protein functionality has been limited by the scarcity and difficulty of obtaining crystal structures of desired proteins. On the other hand, when high‐throughput selection is possible, directed evolution‐based approaches for gaining protein functionalities have been random and fortuitous with limited rationalization. We combine comparative modeling of dimer structures, ab initio loop reconstruction, and ligand docking to select positions for mutagenesis to create a library focused on the ligand‐contacting residues. The rationally reduced library requirement enabled conservative control of the substitutions by oligonucleotide synthesis and bounding its size within practical transformation efficiencies (∼107 variants). This rational approach was successfully applied on an inducer‐binding domain of an Acinetobacter transcription factor (TF), pobR, which shows high specificity for natural effector molecule, 4‐hydroxy benzoate (4HB), but no native response to 3,4‐dihydroxy benzoate (34DHB). Selection for mutants with high transcriptional induction by 34DHB was carried out at the single‐cell level under flow cytometry (via green fluorescent protein expression under the control of pobR promoter). Critically, this selection protocol allows both selection for induction and rejection of constitutively active mutants. In addition to gain‐of‐function for 34DHB induction, the selected mutants also showed enhanced sensitivity and response for 4HB (native inducer) while no sensitivity was observed for a non‐targeted but chemically similar molecule, 2‐hydroxy benzoate (2HB). This is unique application of the Rosetta modeling protocols for library design to engineer a TF. Our approach extends applicability of the Rosetta redesign protocol into regimes without a priori precision structural information. Proteins 2015; 83:1327–1340. © 2015 Wiley Periodicals, Inc.
Structural diversity of the epigenetics pocketome
Authors: Cabaye Alexandre , Nguyen Kong T , Liu Lihua , Pande Vineet , Schapira Matthieu 
Published: May 2015

ABSTRACTProtein families involved in chromatin‐templated events are emerging as novel target classes in oncology and other disease areas. The ability to discover selective inhibitors against chromatin factors depends on the presence of structural features that are unique to the targeted sites. To evaluate challenges and opportunities toward the development of selective inhibitors, we calculated all pair wise structural distances between 575 structures from the protein databank representing 163 unique binding pockets found in protein domains that write, read or erase post‐translational modifications on histones, DNA, and RNA. We find that the structural similarity of binding sites does not always follow the sequence similarity of protein domains. Our analysis reveals increased risks of activity across target‐class for compounds competing with the cofactor of protein arginine methyltransferases, lysine acetyltransferases, and sirtuins, while exploiting the conformational plasticity of a protein target is a path toward selective inhibition. The structural diversity landscape of the epigenetics pocketome can be explored via an open‐access graphic user interface at thesgc.org/epigenetics_pocketome. Proteins 2015; 83:1316–1326. © 2015 Wiley Periodicals, Inc.