bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recombinant reflectin‐based optical materials
Authors: Qin Guokui , Dennis Patrick B. , Zhang Yuji , Hu Xiao , Bressner Jason E. , Sun Zhongyuan , Crookes‐Goodson Wendy J. , Naik Rajesh R. , Omenetto Fiorenzo G. , Kaplan David L. 
Published: November 2012

AbstractReflectins are a unique group of structural proteins involved in dynamic optical systems in cephalopods that modulate incident light or bioluminescence. We describe cloning, structural characterization, and optical properties of a reflectin‐based domain, refCBA, from reflectin 1a of Hawaiian bobtail squid, Euprymna scolopes. Thin films created from the recombinant protein refCBA display interesting optical features when the recombinant protein is appropriately organized. RefCBA was cloned and expressed as a soluble protein enabling purification, with little structural organization found using Fourier transform infrared spectroscopy and circular dichroism. Single‐layer and multi‐layer thin films of refCBA were then produced by flow coating and spin coating, and displayed colors due to thin film interference. Diffraction experiments showed the assemblies were ordered enough to work as diffraction gratings to generate diffraction patterns. Nano‐spheres and lamellar microstructures of refCBA samples were observed by scanning electron microscopy and atomic force microscopy. Despite the reduced complexity of the refCBA protein compared to natural reflectins, unique biomaterials with similar properties to reflectins were generated by self‐assembled reflectin‐based refCBA molecules. © 2012 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2013
Influence of thermal history on mesoscale ordering in polydomain smectic networks
Authors: Chen Huipeng , Yu Ziniu , Hedden Ronald C. 
Published: November 2012

AbstractDramatic changes in mesoscale ordering and macroscopic mechanical behavior are observed in smectic polydomain networks after annealing at a temperature well above the glass transition temperature but below the clearing temperature. Tensile testing reveals gradual stiffening and loss of extensibility, and X‐ray linewidth measurements confirm that stiffening is initially due to thickening of domains. At long annealing times, a more highly ordered smectic mesophase forms, further stiffening the networks and reducing their extensibility. Increasing the concentration of (flexible) crosslinkers hinders domain growth and suppresses formation of the higher order mesophase, a useful guideline for design of smectic networks that exhibit reduced sensitivity to thermal history. © 2012 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2013
Prevalence and predictors of post‐traumatic stress symptoms in adolescent and young adult cancer survivors: a 1‐year follow‐up study
Authors: Kwak Minyoung , Zebrack Brad J. , Meeske Kathleen A. , Embry Leanne , Aguilar Christine , Block Rebecca , Hayes‐Lattin Brandon , Li Yun , Butler Melissa , Cole Steven 
Published: November 2012

AbstractObjectivesPost‐traumatic stress symptoms (PTSS) have been identified as a meaningful indicator of distress in cancer survivors. Distinct from young adult survivors of childhood cancer, young people diagnosed with cancer as adolescents and young adults (AYAs) face unique psychosocial issues; however, there is little published research of PTSS in the AYA population. This study examines prevalence and predictors of PTSS among AYAs with cancer.MethodsAs part of a longitudinal study of AYAs with cancer, 151 patients aged 15–39 years completed mailed surveys at 6 and 12 months post‐diagnosis. Severity of PTSS was estimated at 6 and 12 months post‐diagnosis. Multiple regression analyses were conducted to investigate the predictive effects of socio‐demographic and clinical characteristics on changes in PTSS over time.ResultsAt 6 and 12 months, respectively, 39% and 44% of participants reported moderate to severe levels of PTSS; 29% had PTSS levels suggestive of post‐traumatic stress disorder. No significant differences in severity of PTSS between 6 and 12 months were observed. Regression analyses suggested that a greater number of side effects were associated with higher levels of PTSS at 6 months. Currently receiving treatment, having surgical treatment, diagnosis of a cancer type with a 90–100% survival rate, remaining unemployed/not in school, and greater PTSS at 6 months were associated with higher levels of PTSS at 12 months.ConclusionsPost‐traumatic stress symptoms were observed as early as 6 months following diagnosis and remained stable at 12‐month follow‐up. The development of early interventions for reducing distress among AYA patients in treatment is recommended.Copyright © 2012 John Wiley & Sons, Ltd.
Palivizumab immunoprophylaxis effectiveness in children with cystic fibrosis
Authors: Winterstein Almut G. , Eworuke Efe , Xu Dandan , Schuler Pamela 
Published: November 2012

AbstractBackgroundEvidence on the effectiveness of respiratory syncytial virus (RSV) immunoprophylaxis with palivizumab in children with cystic fibrosis (CF) is lacking.MethodsWe utilized Medicaid Extract files from 27 states from 1999 to 2006 linked to the National Cystic Fibrosis Registry to establish a cohort of children 0–2 years with CF diagnosis. Eligible children entered the cohort after CF diagnosis and after RSV season onset, and were followed until season end, second birthday, death, or hospitalizations for reasons other then the study outcome. Two outcomes were examined: hospitalization for RSV infections (RSV‐ha), or hospitalization for acute respiratory infections (ARI‐ha). Palivizumab exposure was defined based on pharmacy or procedure claims as current (claim date plus 30 days), former (day 31–60 after a claim), and no exposure (days before the first or >60 days after any claim). Both outcomes were examined in a Cox regression model, adjusting for RSV risk factors and CF severity via exposure propensity score.ResultsThe matched cohort included 1,974 infants (2,875 infant seasons), who experienced 32 RSV‐ha and 212 ARI‐ha (3.9 and 26.2/1,000 season months, respectively). Compared to periods of no use, the adjusted hazard ratio for current use was 0.57 (95% confidence interval [CI]: 0.20–1.60) for RSV‐related hospitalization and 0.85 (95% CI: 0.59–1.21) for ARI‐related hospitalization. Each month of increasing age reduced the ARI‐ha by 5.8%.ConclusionRSV hospitalization incidence was low suggesting either little contribution of the virus to respiratory infections in patients with CF or lack of RSV testing. Unadjusted and adjusted RSV‐hospitalization incidence rates suggested potentially positive effects of palivizumab, but results were inconclusive due to small event rates. Hospitalizations for acute respiratory illness with possible RSV contribution showed no association with palivizumab use, suggesting limited overall effect of palivizumab. Younger age greatly increased infection risk. Pediatr Pulmonol. 2013; 48:874–884. © 2012 Wiley Periodicals, Inc.
The BMPR2 missense mutation p.K230N and pulmonary arterial hypertension
Authors: Hayes Don , Ramanathan Chandar , Kopp Benjamin T. 
Published: November 2012

AbstractWe present a patient that is the index case of pulmonary arterial hypertension (PAH) in a child due to the bone morphogenetic protein type II (BMPR2) missense mutation p.K230N, also known as c.690A>T. Missense mutations typically have earlier onset and more severe disease in PAH, so pulmonologists should be aware of this in the evaluation of PAH in children. Pediatr Pulmonol. 2014; 49:E5–E6. © 2013 Wiley Periodicals, Inc.
Structure and function of the SPRY/B30.2 domain proteins involved in innate immunity
Authors: D'Cruz Akshay A. , Babon Jeffrey J. , Norton Raymond S. , Nicola Nicos A. , Nicholson Sandra E. 
Published: November 2012

AbstractThe SPRY domain is a protein interaction module found in 77 murine and ∼100 human proteins, and is implicated in important biological pathways, including those that regulate innate and adaptive immunity. The current definition of the SPRY domain is based on a sequence repeat discovered in the splA kinase and ryanodine receptors. The greater SPRY family is divided into the B30.2 (which contains a PRY extension at the N‐terminus) and “SPRY‐only” sub‐families. In this brief review, we examine the current structural and biochemical literature on SPRY/B30.2 domain involvement in key immune processes and highlight a PRY‐like 60 amino acid region in the N‐terminus of “SPRY‐only” proteins. Phylogenetic, structural, and functional analyses suggest that this N‐terminal region is related to the PRY region of B30.2 and should be characterized as part of an extended SPRY domain. Greater understanding of the functional importance of the N‐terminal region in “SPRY only” proteins will enhance our ability to interrogate SPRY interactions with their respective binding partners.
Crystal structure of Jararacussin‐I: The highly negatively charged catalytic interface contributes to macromolecular selectivity in snake venom thrombin‐like enzymes
Authors: Ullah A. , Souza T. A. C. B. , Zanphorlin L. M. , Mariutti R. B. , Santana V. S. , Murakami M. T. , Arni R. K. 
Published: November 2012

AbstractSnake venom serine proteinases (SVSPs) are hemostatically active toxins that perturb the maintenance and regulation of both the blood coagulation cascade and fibrinolytic feedback system at specific points, and hence, are widely used as tools in pharmacological and clinical diagnosis. The crystal structure of a thrombin‐like enzyme (TLE) from Bothrops jararacussu venom (Jararacussin‐I) was determined at 2.48 Å resolution. This is the first crystal structure of a TLE and allows structural comparisons with both the Agkistrodon contortrix contortrix Protein C Activator and the Trimeresurus stejnegeri plasminogen activator. Despite the highly conserved overall fold, significant differences in the amino acid compositions and three‐dimensional conformations of the loops surrounding the active site significantly alter the molecular topography and charge distribution profile of the catalytic interface. In contrast to other SVSPs, the catalytic interface of Jararacussin‐I is highly negatively charged, which contributes to its unique macromolecular selectivity.
Growth kinetics of CD133‐positive prostate cancer cells
Authors: Reyes Edwin E. , Kunovac Stefan K. , Duggan Ryan , Kregel Steven , Griend Donald J. Vander 
Published: November 2012

AbstractBACKGROUNDIn the adult human prostate CD133 expression is thought to mark rare prostate epithelial stem cells and malignant tumor stem/initiating cells. Such putative stem cell populations are thought to proliferate slowly, but possess unlimited proliferative potential. Based on this, we hypothesized that CD133pos prostate cancer cells proliferate slower than CD133neg cells.METHODSHuman prostate cancer cell lines were analyzed for CD133 expression and DNA content using flow cytometry. Rates of cell division and DNA synthesis were determined using CFSE cell tracing and BrdU uptake, respectively. Changes in cell cycle distribution and the percentage of CD133pos cells were assayed under conditions of different cell density and AR‐pathway modulation. Lastly, we over‐expressed lentiviral CD133 to measure whether CD133 regulates the cell cycle.RESULTSThe cell cycle distribution differs between CD133pos and CD133neg cells in all three human prostate cancer cell lines studied. CD133pos cells have a greater proportion of cells in G2 and proliferate faster than CD133neg cells. High cell density increases the percentage of CD133pos cells without changing CD133pos cell cycle progression. Treatment with the AR agonist R1881, or the anti‐androgen MDV3100, significantly changed the percentage and proliferation of CD133pos cells. Finally, ectopic over‐expression of CD133 had no effect on cell cycle progression.CONCLUSIONSContrary to our hypothesis, we demonstrate that CD133pos cells proliferate faster than CD133neg cells. This association of CD133 expression with increased cell proliferation is not directly mediated by CD133, suggesting that surface CD133 is a downstream target gene of an undefined pathway controlling cell proliferation. Prostate 73: 724–733, 2013. © 2012 Wiley Periodicals, Inc.
Differentiation of isomeric pentose disaccharides by electrospray ionization tandem mass spectrometry and discriminant analysis
Authors: da Costa Elisabete V. , Moreira Ana S. P. , Nunes Fernando M. , Coimbra Manuel A. , Evtuguin Dmitry V. , Domingues M. Rosário M. 
Published: November 2012

RATIONALEThe structural characterization of unknown oligosaccharides remains a big challenge since a large number of isomeric structures are possible even for disaccharides. In this work, electrospray ionization collision‐induced dissociation tandem mass spectrometry (ESI‐CID‐MS/MS) was used for the differentiation of isomeric pentose disaccharides, α‐(1 → 5)‐l‐arabinobiose (Ara2) and β‐(1 → 4)‐d‐xylobiose (Xyl2).METHODSESI‐MS/MS spectra of [M + Li]+ and [M + Na]+ ions of Ara2 and Xyl2, as well as these precursor ions of 18O‐labelled disaccharides, were acquired using two mass spectrometers equipped with different analyzers: LIT (linear ion trap) and Q‐TOF (quadrupole time‐of‐flight).RESULTSProduct ions observed in MS/MS spectra arise from the cleavage at the nonreducing side of the glycosidic bond (Y1+) and from cross‐ring cleavages 0,1A2+, 0,2A2+, and 0,3A2+ at the reducing residue. Statistically significant differences were observed between the relative abundance of specific product ions, when comparing both disaccharides. These differences allowed discriminant models to be built and to propose a criterion using the relative abundances of selected ions capable of discriminating between the isomers for both adduct ions and spectrometers.CONCLUSIONSIsomeric pentose disaccharides can be distinguished based on the fragmentation of both [M + Li]+ and [M + Na]+ ions and using different mass spectrometers. However, LIT instrument has a better discriminant power. Copyright © 2012 John Wiley & Sons, Ltd.
Simulated gastrointestinal digestion of Pru ar 3 apricot allergen: Assessment of allergen resistance and characterization of the peptides by ultra‐performance liquid chromatography/electrospray ionisation mass spectrometry
Authors: Prandi Barbara , Farioli Laura , Tedeschi Tullia , Pastorello Elide Anna , Sforza Stefano 
Published: November 2012

RATIONALENon‐specific lipid transfer proteins (ns‐LTPs) are major food allergens of the Rosaceæ family. The severity of allergic reactions often relates to resistance of the allergen to digestion. Thus, it is important to evaluate the digestibility of these proteins and characterise the peptides generated in the gastrointestinal tract.METHODSSimulated gastrointestinal digestion of purified allergen Pru ar 3 was performed using pepsin for the gastric phase in aqueous HCl at pH = 2 and chymotrypsin and trypsin for the intestinal phase in aqueous NH4HCO3 at pH = 7.8. The peptide mixture obtained was analysed by ultra‐performance liquid chromatography/electrospray ionisation mass spectrometry (UPLC/ESI‐MS). Peptide sequences were identified by comparing their molecular mass to that obtained by in silico digestion, and were confirmed by the ions obtained by in‐source fragmentation. Semi‐quantification was performed for the intact protein by comparison with internal standards.RESULTSThe resistance to gastrointestinal digestion of Pru ar 3 allergen was evaluated to be 9%. This value is consistent with that found for grape LTP, but much lower than the resistance found for peach LTP (35%). All the peptides generated were identified by ESI‐MS on the basis of their molecular mass and from the ions generated from in‐source fragmentation. Apart from low molecular mass peptides, five high molecular mass peptides (4500–7000 Da) containing disulphide bridges were identified. ESI‐MS of the intact protein indicated a less compact folded structure when compared to that of the homologous peach LTP.CONCLUSIONSAn extensive characterisation of the peptides generated from the gastrointestinal digestion of Pru ar 3 allergen was performed here for the first time via UPLC/ESI‐MS analysis. The digestibility of the allergen was evaluated and compared with that of other LTPs, demonstrating that only a small amount of undigested protein remains, and that specific proteolytic action involves immunodominant epitopes. These data might explain the lower allergenicity of apricot LTP compared to peach LTP, despite their high sequence homology. Copyright © 2012 John Wiley & Sons, Ltd.
Pressure baseline correction and high‐precision CO2 clumped‐isotope (∆47) measurements in bellows and micro‐volume modes
Authors: He Bo , Olack Gerard A. , Colman Albert S. 
Published: November 2012

RATIONALECO2 ‘clumped‐isotope’ measurements (tracking enrichment of 16O13C18O, reported as ∆47 values, on CO2 derived from carbonate minerals or the atmosphere) are becoming central to a wide range of geochemical investigations. We present a novel approach to address problems with instrument stability, external precision, and the analysis of small samples that have hampered the advancement of Δ47 measurements.METHODSWe measured Δ47 values on CO2 gases introduced via dual inlet to an isotope ratio mass spectrometer. We developed a method for determining the 'pressure baseline' and integrating a correction to ion beam intensity measurements during analysis. We then tested this approach for both bellows and micro‐volume modes of sample introduction. Heated gas and equilibrated gas lines (Δ47 vs. δ47) established the effectiveness of this correction.RESULTSWe have determined that drift in instrument calibration that compromises Δ47 measurements results from a shift in the baseline signal on sensitive collectors (m/z 47, 48, and 49) that occurs when gas is admitted to the ion source. Applying a 'pressure baseline' (PBL) correction significantly stabilizes ∆47 measurements and reduces the dependence of ∆47 values on δ47 values by up to an order of magnitude.CONCLUSIONSPBL‐corrected heated gas and equilibrated gas calibrations in bellows and micro‐volume modes are nearly identical and stable through time. Introduction of the PBL correction, a revision to the absolute reference frame approach to determining Δ47 values, dramatically improves the external precision of Δ47 measurements to near instrumental analytical uncertainty (6–8 ppm (1σ) in bellows mode; 10–12 ppm in micro‐volume mode). Copyright © 2012 John Wiley & Sons, Ltd.
Coke Reactivity under Blast Furnace Conditions and in the CSR/CRI Test
Authors: Lundgren Maria , Sundqvist Ökvist Lena , Björkman Bo 
Published: November 2012

AbstractThe present work aims to study the high‐temperature strength of coke. Mechanisms of disintegration were evaluated using basket samples charged into LKAB's experimental blast furnace prior to quenching and dissection. Coke charged into basket samples was analysed with CSR/CRI tests and compared with treated coke from the blast furnace. Results from tumbling tests, chemical analyses of coarse and fine material, as well as light optical microscopy studies of original and treated coke have been combined and evaluated. The results indicate a correlation between the ash composition and the CSR values. Differences in the texture of the coke were noted with light optical microscopy, and a significant change in the coke texture during the CSR/CRI test conditions was found. The results suggest that the main reaction between coke and CO2 took place in isotropic areas, which was especially pronounced in coke with a low CSR. Signs of degradation were apparent throughout the coke pieces that have undergone CSR/CRI testing, but were less observable in coke reacted in the blast furnace. The results indicate that reaction with CO2 is generally limited by the chemical reaction rate in the CSR/CRI test, while in the blast furnace the reaction is limited by the diffusion rate. Coke degradation is therefore mostly restricted to the coke surface in the blast furnace.
Local people's accounts of climate change: to what extent are they influenced by the media?
Authors: Marin Andrei , Berkes Fikret 
Published: November 2012

AbstractResearchers using local and indigenous people's accounts of climate change in their scientific work often face scepticism regarding the value of such information. The critics' argument is that since local and indigenous people are often exposed to the global discourse on climate change, their observations and information may in fact be reproductions of science popularized through communication media. There are instances in which local people's accounts of climate change and impacts thereof may be influenced by how media frame and popularize scientific models and predictions. However, we propose several reasons why the influence of media reports and coverage of climate change is usually superficial. First, there are significant differences between the epistemologies employed by media and those of local people. Although media may be borrowing local environmental categories, they may be filling them with different content, leading to incoherence. Second, media accounts are often general and locally irrelevant, in contrast with the detailed local anchoring of the knowledge often held by people who rely on natural resources for their livelihoods. Their observations often rely on holistic ways of knowing their environments, integrating large numbers of variables, and the relationships between these. We propose that accounts based on such observations are probably not influenced by media framings and that uncovering their underlying ‘ways of knowing’ would provide valuable additional evidence in interdisciplinary studies of climate change. WIREs Clim Change 2013, 4:1–8. doi: 10.1002/wcc.199This article is categorized under:

Social Status of Climate Change Knowledge > Sociology/Anthropology of Climate Knowledge
Transfer RNA modifications: nature's combinatorial chemistry playground
Authors: Jackman Jane E. , Alfonzo Juan D. 
Published: November 2012

AbstractFollowing synthesis, tRNAs are peppered by numerous chemical modifications which may differentially affect a tRNA's structure and function. Although modifications affecting the business ends of a tRNA are predictably important for cell viability, a majority of modifications play more subtle structural roles that can affect tRNA stability and folding. The current trend is that modifications act in concert and it is in the context of the specific sequence of a given tRNA that they impart their differing effects. Recent developments in the modification field have highlighted the diversity of modifications in tRNA. From these, the combinatorial nature of modifications in explaining previously described phenotypes derived from their absence has emerged as a growing theme. WIREs RNA 2013, 4:35–48. doi: 10.1002/wrna.1144This article is categorized under:

RNA Processing > RNA Editing and Modification
RNA Processing > tRNA Processing