bluuebunny/crossref_metadata_2025 huggingface dataset:
Transparent thermoplastic resin with electron beam cross‐linking
Authors: Sano Tomomi , Nakabayashi Makoto , Ito Hiroshi
Published: October 2011

The mechanical, thermal and optical properties of a transparent thermoplastic resin which is based on non‐crystalline nylon with cross‐linking agents were improved by electron beam (EB) irradiation cross‐linking. When the EB irradiation power was increased, the yield stress improved by 34% and the glass transformation temperature increased from 116 to 165°C. Transformation from the brittle to the ductile state was observed by the dependence of a strange elastic module on the temperature and EB irradiation power. Above the glass transformation temperature, an optical element produced using this resin could maintain its shape. The birefringence decreased when the EB irradiation power was increased. The decrease of the birefringence was dependent on the initial birefringence value before EB cross‐linking. The molecular orientation was relaxed by EB cross‐linking. POLYM. ENG. SCI., 2012. © 2011 Society of Plastics Engineers
Velocity measurements on a polypropylene melt during extrusion through a flat coat‐hanger die
Authors: Grieß Hans Jürgen , Burghelea Teodor I. , Münstedt Helmut
Published: October 2011

An experimental investigation of various flow regimes observed during the extrusion of a polypropylene melt through a flat coat‐hanger die by laser‐Doppler velocimetry (LDV) is presented. LDV measurements of the velocity profiles across the gap of the die at various locations along the die reveal three different extrusion regimes. At small wall shear stresses, the velocity profiles can be fitted by symmetrical curves with the velocities becoming zero at the die walls. These profiles are not uniformly distributed along the die. An increase of the wall shear stress reveals a second flow regime characterized by a uniform distribution of the velocity profiles along the die. As the wall shear stress is increased even further, a third flow regime characterized by wall slip on the glass windows is observed. This flow regime is systematically characterized by measurements of the slip velocities at various temperatures and throughputs. The maximum velocities along the die are taken to assess the uniformity of flow which decisively influences the thickness of the extruded film. By measuring velocity profiles, at different throughput, and temperatures, the conditions for constant velocities along the die were determined. POLYM. ENG. SCI., 2012. © 2011 Society of Plastics Engineers
Melt grafting of maleic anhydride onto polypropylene with assistance of α‐methylstyrene
Authors: Luo Weihua , Liu Xingxing , Fu Yujuan
Published: October 2011

Melt grafting of maleic anhydride (MA) and α‐methylstyrene (AMS) onto polypropylene (PP) was performed by reactive extrusion. Effects of AMS on the graft degree of MA, crystallization behavior, and thermal properties of the graft copolymer were investigated. Results show that the addition of AMS as a comonomer can efficiently improve the MA graft degree. When the molar ratio of AMS to MA is 0.9:1, the maximum MA graft degree is attained, which increases about 56% compared with that using single monomer of MA. The results of the graft degree of MA obtained by chemical titration (CT) agree well with those obtained by Fourier transform infrared spectroscopy (FTIR). Melt flow rate (MFR) measurements indicate that the addition of AMS effectively reduces the degradation of PP molecules. The wide‐angle X‐ray diffraction (WAXD) results show that in comparison with the PP‐g‐MA sample, the PP‐g‐(MA‐AMS) sample shows no new crystalline form, but has a slight decrease in the average crystalline domain size. According to the results of thermogravimetry (TG) and differential scanning calorimetry (DSC), the graft PP in the presence of AMS exhibits a lower melting point and a higher crystallization temperature and thermal stability in comparison with that without AMS. POLYM. ENG. SCI., 2011. © 2011 Society of Plastics Engineers
Effects of phosphate and polysiloxane on flame retardancy and impact toughening behavior of poly(2,6‐dimethyl‐1,4‐phenylene oxide)
Authors: Lin Shiwen , Sun Shuangyue , He Yadong , Wang Xiaodong , Wu Dezhen
Published: October 2011

Poly(2,6‐dimethyl‐1,4‐phenylene oxide) (PPO)‐based compounds containing resorcinol bis(diphenyl phosphate) (RDP) and poly(dimethyl‐diphenyl siloxane) (PDMDPS) were prepared through melt extrusion, and their flammability characteristics and mechanical properties were evaluated. The incorporation of RDP enhanced the flame retardancy of PPO compounds, but hardly made them obtain the UL 94 V‐0 rating unless RDP and PDMDPS were combined. Studies on the residual chars after vertical burning test suggested that the excellent flame retardancy be correlated with the retention from the combination effects of silica and phosphate in the char, whose cross‐linked silica enhanced the formation of a compact char to retard combustion. Thermogravimetric analysis indicated that the presence of PDMDPS and RDP improved the char yielding as well as the decomposition temperature of PPO compounds. Moreover, the Izod impact strength was improved significantly in the presence of RDP and PDMDPS, and this toughening effect was attributed to the deformation and multiple cracks induced by PDMDPS, which enhances the impact energy absorption of the matrix. This work provides a very effective flame retarding formulation for PPO compounds with improved impact toughness. POLYM. ENG. SCI., 2012. © 2011 Society of Plastics Engineers
The ErbB4 extracellular region retains a tethered‐like conformation in the absence of the tether
Authors: Liu Ping , Bouyain Samuel , Eigenbrot Charles , Leahy Daniel J.
Published: October 2011

The epidermal growth factor receptor (EGFR) and its homologs ErbB3 and ErbB4 adopt a tethered conformation in the absence of ligand in which an extended hairpin loop from domain II contacts the juxtamembrane region of domain IV and tethers the domain I/II pair to the domain III/IV pair. By burying the hairpin loop, which is required for formation of active receptor dimers, the tether contact was thought to prevent constitutive activation of EGFR and its homologs. Amino‐acid substitutions at key sites within the tether contact region fail to result in constitutively active receptors however. We report here the 2.5 Å crystal structure of the N‐terminal three extracellular domains of ErbB4, which bind ligand but lack domain IV and thus the tether contact. This ErbB4 fragment nonetheless adopts a domain arrangement very similar to the arrangement adopted in the presence of the tether suggesting that regions in addition to the tether contribute to maintaining this conformation and inactivity in the absence of the tether contact. We suggest that the tether conformation may have evolved to prevent crosstalk between different EGFR homologs and thus allow diversification of EGFR and its homologs.
Temperature‐dependent study reveals that dynamics of hydrophobic residues plays an important functional role in the mitochondrial Tim9–Tim10 complex
Authors: Ivanova Ekaterina , Pang Jiayun , Jowitt Thomas A. , Yan Guanhua , Warwicker Jim , Sutcliffe Michael J. , Lu Hui
Published: October 2011

Protein–protein interaction is a fundamental process in all major biological processes. The hexameric Tim9–Tim10 (translocase of inner membrane) complex of the mitochondrial intermembrane space plays an essential chaperone‐like role during import of mitochondrial membrane proteins. However, little is known about the functional mechanism of the complex because the interaction is weak and transient. This study investigates how electrostatic and hydrophobic interactions affect the conformation and function of the complex at physiological temperatures, using both experimental and computational methods. The results suggest that, first, different complex conformational states exist at equilibrium, and the major difference between these states is the degree of hydrophobic interactions. Second, the conformational change mimics the biological activity of the complex as measured by substrate binding at the same temperatures. Finally, molecular dynamics simulation and detailed energy decomposition analysis provided supporting evidence at the atomic level for the presence of an excited state of the complex, the formation of which is largely driven by the disruption of hydrophobic interactions. Taken together, this study indicates that the dynamics of the hydrophobic residues plays an important role in regulating the function of the Tim9–Tim10 complex. Proteins 2012. © 2011 Wiley Periodicals, Inc.
Ligand‐induced formation of transient dimers of mammalian 12/15‐lipoxygenase: A key to allosteric behavior of this class of enzymes?
Authors: Ivanov Igor , Shang Weifeng , Toledo Lea , Masgrau Laura , Svergun Dmitri I. , Stehling Sabine , Gómez Hansel , Di Venere Almerinda , Mei Giampiero , Lluch José M. , Skrzypczak‐Jankun Ewa , González‐Lafont Àngels , Kühn Hartmut
Published: October 2011

Mammalian lipoxygenases (LOXs) have been implicated in cellular defense response and are important for physiological homeostasis. Since their discovery, LOXs have been believed to function as monomeric enzymes that exhibit allosteric properties. In aqueous solutions, the rabbit 12/15‐LOX is mainly present as hydrated monomer but changes in the local physiochemical environment suggested a monomer–dimer equilibrium. Because the allosteric character of the enzyme can hardly be explained using a single ligand binding‐site model, we proposed that the binding of allosteric effectors may shift the monomer–dimer equilibrium toward dimer formation. To test this hypothesis, we explored the impact of an allosteric effector [13(S)‐hydroxyoctadeca‐9(Z),11(E)‐dienoic acid] on the structural properties of rabbit 12/15‐LOX by small‐angle X‐ray scattering. Our data indicate that the enzyme undergoes ligand‐induced dimerization in aqueous solution, and molecular dynamics simulations suggested that LOX dimers may be stable in the presence of substrate fatty acids. These data provide direct structural evidence for the existence of LOX dimers, where two noncovalently linked enzyme molecules might work in unison and, therefore, such mode of association might be related to the allosteric character of 12/15‐LOX. Introduction of negatively charged residues (W181E + H585E and L183E + L192E) at the intermonomer interface disturbs the hydrophobic dimer interaction of the wild‐type LOX, and this structural alteration may lead to functional distortion of mutant enzymes. Proteins 2011. © 2012 Wiley Periodicals, Inc.
Quantification of the Sorption Behavior of Polyethylene Terephthalate Polymer versus PET/PA Polymer Blends towards Organic Compounds
Authors: Welle F. , Bayer F. , Franz R.
Published: October 2011

Polyethylene terephthalate (PET) bottles are widely used for beverages. Oxygen‐sensitive beverages, however, often require the use of barrier materials or oxygen‐scavenging additives incorporated into the PET material, which is in most cases polyamide (PA). As a consequence, small amounts of polyamide are entering the PET bottle‐to‐bottle recycling feedstream. Aim of the study was therefore the determination of the sorption behavior of bottles made of different PET/PA blends in comparison with a PET reference. As a result, PET test bottles containing blended PA amounts of up to 1000 ppm do not show a sorption behavior for the investigated model compounds, which is different from pure PET material. Therefore, polyamide impurities in the recycling streams coming from polyamide barrier bottles will not lead to a different sorption/remigration behavior as pure PET bottles. Consequently, evaluations of PET recycling processes will still be valid for feedstream materials containing such small amounts of polyamide from barrier bottles. On the other hand, the introduction of 8% of polyamide decreases significantly the sorption of organic compounds into the bottle wall. Copyright © 2011 John Wiley & Sons, Ltd.
Separation of peptides from detergents using ion mobility spectrometry
Authors: Bagag Aïcha , Giuliani Alexandre , Canon Francis , Réfrégiers Matthieu , Naour François Le
Published: October 2011

Mass spectrometry (MS) has dramatically evolved in the last two decades and has been the driving force of the spectacular expansion of proteomics during this period. However, the very poor compatibility of MS with detergents is still a technical obstacle in some studies, in particular on membrane proteins. Indeed, the high hydrophobicity of membrane proteins necessitates the use of detergents for their extraction and solubilization. Here, we address the analytical potential of high‐field asymmetric waveform ion mobility spectrometry (FAIMS) for separating peptides from detergents. The study was focused on peptides from the human integral membrane protein CD9. A tryptic peptide was mixed with the non‐ionic detergents Triton X‐100 or beta‐D‐dodecyl maltoside (DDM) as well as with the ionic detergents sodium dodecyl sulfate (SDS) or sodium deoxycholate (SDC). Although electrospray ionization (ESI) alone led to a total suppression of the peptide ion signal on mass spectra with only detection of the detergents, use of FAIMS allowed separation and clear identification of the peptide with any of the detergents studied. The detection and identification of the target compound in the presence of an excess of detergents are then feasible. FAIMS should prove especially useful in the structural and proteomic analysis of membrane proteins. Copyright © 2011 John Wiley & Sons, Ltd.
Detection and identification of alkylphosphonic acids by positive electrospray ionization tandem mass spectrometry using a tricationic reagent
Authors: Tak Vijay , Pardasani Deepak , Purohit Ajay , Dubey D. K.
Published: October 2011

The retrospective detection and identification of degradation products of chemical warfare agents are of immense importance in order to prove their spillage and use. A highly sensitive liquid chromatography/electrospray ionization tandem mass spectrometric (LC/ESI‐MS/MS) method – using an imidazolium‐based tricationic reagent – was developed for the detection and identification of the anionic degradation products of nerve agents. A commercially available solution of 1,3‐imidazolium‐bis‐(1‐hexylbenzylimidazolium) trifluoride (IBHBI) formed adducts with alkylphosphonic acids (APAs), allowing detection of the APAs by positive mode ESI‐MS. Tandem mass spectrometry was used for the unambiguous identification of the APAs. Parameters influencing the formation and stability of these adduct during mass spectrometric analysis, such as solvent composition, concentration of IBHBI, effect of pH and interferences by salts, were optimized. The absolute limits of detection (0.1 ng) for achieved for the APAs were better than those previously reported, and linear dynamic ranges of 10–2000 ng mL–1 were achieved. The method was repeatable with a relative standard deviation ≤7.3%. APAs present in aqueous samples provided by the Organization for the Prohibition of Chemical Weapons during the 22nd and 24th Official Proficiency tests were detected and identified as IBHBI adducts. The added advantage of this method is that low‐mass analytes are detected at higher mass, thus obviating the problem with background noise at low mass. Copyright © 2011 John Wiley & Sons, Ltd.
From implant planning to surgical execution: an integrated approach for surgery in oral implantology
Authors: Chiarelli Tommaso , Franchini Federico , Lamma Achille , Lamma Evelina , Sansoni Tommaso
Published: October 2011

Background

Using oral implantology software and transferring the preoperative planning into a stereolithographic model, prosthodontists can produce the related surgical guide. This procedure has some disadvantages: bone‐supported stent invasiveness, lack of references due to scattering and non‐negligible stereolithography cost. An alternative solution is presented that provides an ideal surgical stent (not invasive, precise, and cheap) as a result. This work focuses on the third phase of a fully 3D approach to oral implant planning, that starts by CT scanning a patient who wears a markers‐equipped radiological stent, continues exploiting built‐on‐purpose preoperative planning software, and finishes producing the ideal surgical template.

Methods

A 5‐axes bur‐equipped robot has been designed able to reproduce the milling vectors planned by the software. Software–robot interfacing has been achieved properly matching the stent reference frame and the software and robot coordinate systems. Invasiveness has been avoided achieving the surgical stent from the mucosa‐supported radiological mask wax‐up. Scattering is ignored because of the surgical stent independency from the bone structure radiography. Production cost has been strongly reduced by avoiding the stereolithographic model. Finally, software–robot interfacing precision has been validated comparing digitally a multi‐marker base and its planning transfer.

Results

Average position and orientation errors (respectively 0.283 mm ± 0.073 mm and 1.798° ± 0.496°) were significantly better than those achieved using methods based on stereolithography (respectively, 1.45 mm ± 1.42 mm and 7.25° ± 2.67°, with a general best maximum translation discrepancy of about 1.1 mm).

Conclusions

This paper describes the last step of a fully 3D approach in which implant planning can be done in a 3D environment, and the correct position, orientation and depth of the planned implants are easily computed and transferred to the surgical phase. Copyright © 2011 John Wiley & Sons, Ltd.
Synchronization of epicardial crawling robot with heartbeat and respiration for improved safety and efficiency of locomotion
Authors: Patronik Nicholas A. , Ota Takeyoshi , Zenati Marco A. , Riviere Cameron N.
Published: October 2011

Background

HeartLander is a miniature mobile robot designed to navigate over the epicardium of the beating heart for minimally invasive therapy. This paper presents a technique to decrease slippage and improve locomotion efficiency by synchronizing the locomotion with the intrapericardial pressure variations of the respiration and heartbeat cycles.

Methods

Respiratory and heartbeat phases were detected in real time using a chest‐mounted accelerometer during locomotion in a porcine model in vivo. Trials were conducted over the lateral aspect of the heart surface to test synchronized locomotion against an unsynchronized control.

Results

Offline evaluation showed that the respiration and heartbeat algorithms had accuracies of 100% and 88%, respectively. Synchronized trials exhibited significantly lower friction, higher efficiency, and greater total distance traveled than control trials.

Conclusion

Synchronization of the locomotion of HeartLander with respiration and heartbeat is feasible and results in safer and more efficient travel on the beating heart. Copyright © 2011 John Wiley & Sons, Ltd.
Virtual network stacks: from theory to practice
Authors: Matos Alfredo , Ferreira Rui , Sargento Susana , Aguiar Rui L.
Published: October 2011

Privacy is becoming a pressing requirement that spawns across different network layers and user interactions. Using multiple identifiers for the same user, pseudonyms, as means for preserving privacy, is becoming an important approach that has not seen proper discussion or validation. This paper presents formalization on pseudonymity specially considering its influence on the network stack. It presents a study on privacy requirements and its implementation cost, both at theoretical and practical levels, through the support of multiple network stack instantiations and network identifiers per user. We discuss how pseudonyms can be used to preserve users' privacy, and what key issues and requirements are needed, to use, control, and evaluate a pseudonym‐based solution at network level. The paper further presents an architecture that builds a pseudonym‐based solution supported throughout the network stack, describes its implementation in a real testbed, and depicts the results obtained related to both efficiency and costs of such a privacy approach. Finally, it discusses the characteristics of the architecture according to the identified privacy requirements, its impacts and constraints. Copyright © 2011 John Wiley & Sons, Ltd.
Quantitative Assessment of the Comparative Nanoparticle‐Uptake Efficiency of a Range of Cell Lines
Authors: dos Santos Tiago , Varela Juan , Lynch Iseult , Salvati Anna , Dawson Kenneth A.
Published: October 2011

The mechanism(s) of nanoparticle–cell interactions are still not understood. At present there is little knowledge of the relevant length‐ and timescales for nanoparticle intracellular entry and localization within cells, or the cell‐specificity of nanoparticle uptake and localisation. Here, the effect of particle size on the in‐vitro intracellular uptake of model fluorescent carboxyl‐modified polystyrene nanoparticles is investigated in various cell lines. A range of micro‐ and nanoparticles of defined sizes (40 nm to 2 μm) are incubated with a series of cell types, including HeLa and A549 epithelial cells, 1321N1 astrocytes, HCMEC D3 endothelial cells, and murine RAW 264.7 macrophages. Techniques such as confocal microscopy and flow cytometry are used to study particle uptake and subcellular localisation, making significant efforts to ensure reproducibility in a semiquantitative approach. The results indicate that internalization of (nano)particles is highly size‐dependent for all cell lines studied, and the kinetics of uptake for the same type of nanoparticle varies in the different cell types. Interestingly, even cells not specialized for phagocytosis are able to internalize the larger nanoparticles. Intracellular uptake of all sizes of particles is observed to be highest in RAW 264.7 cells (a specialized phagocytic cell line) and the lowest in the HeLa cells. These results suggest that (nano)particle uptake might not follow commonly defined size limits for uptake processes, and highlight the variability of uptake kinetics for the same material in different cell types. These conclusions have important implications for the assessment of the safety of nanomaterials and for the potential biomedical applications of nanoparticles.
Supporting software architects to improve their software system's decomposition – lessons learned
Authors: Vanya Adam , Klusener Steven , Premraj Rahul , van Vliet Hans
Published: October 2011

The architect of a large, evolving system may wish to revise its decomposition from time to time; for instance, because the structure has deteriorated over time, certain components need to be outsourced to another site. One way to assess the current decomposition is to consider the past evolution, searching for components that often changed together. We iteratively devised and implemented a process for doing so at Philips Healthcare MRI. In this paper, we describe the lessons learned on how to effectively support architects to improve their system decomposition. Copyright © 2011 John Wiley & Sons, Ltd.
Effects of low‐dose exposure to pesticide mixture on physiological responses of the pacific oyster, Crassostrea gigas
Authors: Geret F. , Burgeot T. , Haure J. , Gagnaire B. , Renault T. , Communal P. Y. , Samain J. F.
Published: October 2011

This study investigated the effects on the physiology of Pacific oyster, Crassostrea gigas, of a mixture of pesticides containing 0.8 μg L−1 alachlor, 0.6 μg L−1 metolachlor, 0.7 μg L−1 atrazine, 0.6 μg L−1 terbuthylazine, 0.5 μg L−1 diuron, 0.6 μg L−1 fosetyl aluminum, 0.05 μg L−1 carbaryl, and 0.7 μg L−1 glyphosate for a total concentration of 4.55 μg L−1. The total nominal concentration of pesticides mixture corresponds to the pesticide concentrations in the shellfish culture area of the Marennes‐Oleron basin. Two varieties of C. gigas were selected on the foreshore, based on their characteristics in terms of resistance to summer mortality, to assess the effects of the pesticide mixture after 7 days of exposure under controlled conditions. The early effects of the mixture were assessed using enzyme biomarkers of nitrogen metabolism (GS, glutamine synthetase), detoxification metabolism (GST, glutathione S‐transferase), and oxidative stress (CAT, catalase). Sublethal effects on hemocyte parameters (phagocytosis and esterase activity) and DNA damages (DNA adducts) were also measured. Changes in metabolic activities were characterized by increases in GS, GST, and CAT levels on the first day of exposure for the “resistant” oysters and after 3–7 days of exposure for the “susceptible” oysters. The formation of DNA adducts was detected after 7 days of exposure. The percentage of hemocyte esterase‐positive cells was reduced in the resistant oysters, as was the hemocyte phagocytic capacity in both oyster varieties after 7 days of exposure to the pesticide mixture. This study highlights the need to consider the low doses and the mixture of pesticides to evaluate the effects of these molecules on organisms. © 2011 Wiley Periodicals, Inc. Environ Toxicol 28: 689–699, 2013.
Tomographic ultrasound imaging of the pelvic floor in nulliparous pregnant women: limits of normality
Authors: Adisuroso T. , Shek K. L. , Dietz H. P.
Published: October 2011

Objectives

To define normal appearance of the puborectalis muscle on tomographic ultrasound imaging in pregnant nulliparous women, establishing limits of normality.

Methods

This was a subanalysis of consecutive ultrasound volume datasets of 497 pregnant nulliparous women recruited in the context of two studies. All participants were carrying a singleton pregnancy at a mean gestation of 36.4 (range, 33–38) weeks. Tomographic ultrasound imaging was performed by subsequent post‐processing on volumes obtained at maximal pelvic floor contraction at 2.5‐mm slice intervals, from 5 mm below to 12.5 mm above the plane of minimal hiatal dimensions, producing eight slices per patient.

Results

Apparent abnormalities of the insertion of the puborectalis muscle were commonly seen in slices 1 and 2, but were uncommon in slice 3 (< 8%), very uncommon in slice 4 (1%) and rare elsewhere. They were not associated with bladder neck descent. Considering published minimal criteria for diagnosing an avulsion of the puborectalis muscle (slices 3 to 5 all abnormal), this diagnosis was made in three women. On reviewing those cases, one of which was rated abnormal on both sides, two were false positive as judged by the two senior authors. However, one was judged to be highly abnormal by both senior authors, with a full avulsion diagnosed on the left.

Conclusions

Published minimal criteria for the diagnosis of avulsion of the puborectalis muscle by tomographic pelvic floor ultrasound imaging are highly unlikely to result in a false‐positive diagnosis and appear to be sufficiently robust for clinical practice. Copyright © 2012 ISUOG. Published by John Wiley & Sons, Ltd.
Structure of P2X receptors
Authors: Browne Liam E.
Published: October 2011

P2X receptors are trimeric ion channels that open in response to extracellular ATP. The publication of the first X‐ray structure of a closed P2X receptor has confirmed many of the functional experiments carried out since the mid‐1990s and provides a point of reference for the molecular dissection of P2X receptor function. These co‐ordinates shed light on the ATP binding sites housed in the extracellular domain, the contacts between subunits, the pathways for ion access, and the cation‐selective pore that spans the cell membrane. They also provide a template for structure‐based design of much needed pharmacological agents to act on a receptor superfamily whose physiological roles extend from synaptic transmission to inflammation and control of programmed cell death. Interpretation of functional data in the context of this closed P2X receptor structure reveals structural rearrangements in the transmembrane pore and extracellular domain. Here the current understanding of the molecular structure of P2X receptors is reviewed. This review will be of relevance to those interested in the mechanisms that underlie the molecular operation of P2X receptors, and other ion channels gated by diffusible ligands (pentameric Cys‐loop receptors, tetrameric glutamate receptors), as well as trimeric ion channels that are distantly related to P2X receptors (acid‐sensing ion channels and the epithelial sodium channel). WIREs Membr Transp Signal 2012, 1:56–69. doi: 10.1002/wmts.24

For further resources related to this article, please visit the WIREs website.
Evolution and diversity of opsins
Authors: Terakita Akihisa , Kawano‐Yamashita Emi , Koyanagi Mitsumasa
Published: October 2011

Many animals capture light information via opsin‐based pigments. Several thousands of opsins have been identified thus far and the opsin family is divided into eight groups. Members belonging to four out of the eight groups have been elucidated to couple to transducin, Go, Gs, and Gq, respectively, in photoreceptor cells. Accumulated evidence suggests a novel classification of the animal phototransductions, cyclic nucleotide signaling mediated by transducin, Go or Gs in ciliary photoreceptor cells and phosphoinositol signaling mediated by Gq in rhabdomeric photoreceptor cells. Varied opsin‐based pigments are spectroscopically classified into two types, bleaching and bistable pigments; that is, the photoproduct of vertebrate visual pigments dissociates its chromophore retinal over time and bleaches, whereas most other opsin‐based pigments convert to a stable photoproduct, which can revert to original dark state by subsequent light absorption. Mutational analyses of the both types of pigments implied that during molecular evolution of the vertebrae visual pigments, displacement of the counterion, important amino acid residue for visible light absorption of opsin‐based pigment, resulted in not only unique bleaching property but also acquisition of red‐sensitive visual pigment and higher G‐protein activation ability generated by larger light‐induced conformational change of the pigment. Interestingly, a bleaching pigment rhodopsin and parapinopsin, which closely relates to the vertebrate visual pigment but has a bistable nature, couple to visual arrestin and β arrestin, respectively, in the lamprey pineal organ, suggesting the bleaching property also might facilitate the evolution of visual arrestin which is specialized for vertebrate visual function. WIREs Membr Transp Signal 2012, 1:104–111. doi: 10.1002/wmts.6

For further resources related to this article, please visit the WIREs website.
The mechanism of the second step of pre‐mRNA splicing
Authors: Horowitz David S.
Published: October 2011

The molecular mechanisms of the second step of pre‐mRNA splicing in yeast and higher eukaryotes are reviewed. The important elements in the pre‐mRNA, the participating proteins, and the proposed secondary structures and roles of the snRNAs are described. The sequence of events in the second step is presented, focusing on the actions of the proteins in setting up and facilitating the second reaction. Mechanisms for avoiding errors in splicing are discussed. WIREs RNA 2012, 3:331–350. doi: 10.1002/wrna.112

This article is categorized under:

RNA Processing > Splicing Mechanisms
Signals for pre‐mRNA cleavage and polyadenylation
Authors: Tian Bin , Graber Joel H.
Published: October 2011

Pre‐mRNA cleavage and polyadenylation is an essential step for 3′ end formation of almost all protein‐coding transcripts in eukaryotes. The reaction, involving cleavage of nascent mRNA followed by addition of a polyadenylate or poly(A) tail, is controlled by cis‐acting elements in the pre‐mRNA surrounding the cleavage site. Experimental and bioinformatic studies in the past three decades have elucidated conserved and divergent elements across eukaryotes, from yeast to human. Here we review histories and current models of these elements in a broad range of species. WIREs RNA 2012, 3:385–396. doi: 10.1002/wrna.116

This article is categorized under:

RNA Processing > 3' End Processing
Systems vaccinology: learning to compute the behavior of vaccine induced immunity
Authors: Nakaya Helder I. , Li Shuzhao , Pulendran Bali
Published: October 2011

The goal of systems biology is to access and integrate information about the parts (e.g., genes, proteins, cells) of a biological system with a view to computing and predicting the behavior of the system. The past decade has witnessed technological revolutions in the capacity to make high throughput measurements about the behavior of genes, proteins, and cells. Such technologies are widely used in biological research and in medicine, such as toward prognosis and therapy response prediction in cancer patients. More recently, systems biology is being applied to vaccinology, with the goal of: (1) understanding the mechanisms by which vaccines stimulate protective immunity, and (2) predicting the immunogenicity or efficacy of vaccines. Here, we review the recent advances in this area, and highlight the biological and computational challenges posed. WIREs Syst Biol Med 2012, 4:193–205. doi: 10.1002/wsbm.163

This article is categorized under:

Models of Systems Properties and Processes > Cellular Models
Engineered tissue grafts: opportunities and challenges in regenerative medicine
Authors: Feinberg Adam W.
Published: October 2011

The human body has limited regenerative capacity in most of the major tissues and organs. This fact has spurred the field of regenerative medicine, promising to repair damage following traumatic injury or disease. Multiple therapeutic strategies are being explored including small molecules, gene delivery, and stem cells; however, tissue engineering remains a primary approach to achieving regeneration. Organ transplantation demonstrates that damaged tissues can be replaced, but technology to regenerate complex organs de novo is not yet available. Instead, tissue engineering can augment the body's own regenerative ability by replacing tissue sections and enhancing the regenerative cascade. As a consequence of these opportunities, it is timely to review the criteria and current status of engineered tissue grafts designed as patches to replace or regenerate damaged or diseased tissue and restore organ function. This topic will be explored starting from the biomaterials and cells incorporated into the engineered graft, the environment into which the graft is implanted and the integration of the engineered graft with the host. Common issues will be addressed that are relevant to regeneration in multiple tissue and organ systems. Specific examples will focus on engineered grafts for myocardial and corneal repair to illustrate the tissue‐specific challenges and opportunities and highlight the innovation needed as the field moves forward. WIREs Syst Biol Med 2012, 4:207–220. doi: 10.1002/wsbm.164

This article is categorized under:

Developmental Biology > Stem Cell Biology and Regeneration

Translational, Genomic, and Systems Medicine > Therapeutic Methods

Translational, Genomic, and Systems Medicine > Translational Medicine
Site Preference of Metal Atoms in Gd5–xMxTt4 (M = Zr, Hf; Tt = Si, Ge)
Authors: Yao Jinlei , Mozharivskyj Yurij
Published: October 2011

Zirconium and hafnium were incorporated into the Gd5Ge4 and Gd5Si4 parent compounds in order to study the metal‐site occupation in the M5X4 magnetocaloric phases (M = metals; X = p elements) family. The Gd5–xZrxGe4 phases adopt the orthorhombic Sm5Ge4‐type (space group Pnma) structure for x ≤ 1.49 and the tetragonal Zr5Si4‐type (P41212) structure for x ≥ 1.77. The Gd5–xHfxSi4 compounds crystallize in the orthorhombic Gd5Si4‐type (Pnma) structure forx ≤ 0.41 and the Zr5Si4‐type structure for x ≥ 0.7. In both systems, single‐crystal X‐ray diffraction reveals that the Zr/Hf atoms preferentially occupy the slab‐surface M2 and slab‐center M3 sites, both of which have a significantly larger Zr/Hf population than the slab‐surface M1 site. The metal‐site preference, i.e. the coloring problem on the three metal sites, is discussed considering geometric and electronic effects of the local coordination environments. The analysis of the metal‐site occupation in Gd5–xZrxGe4 and Gd5–xHfxSi4 as well as other metal‐substituted M5X4 systems suggests that both geometric and electronic effects can be used to explain the metal‐site occupation.
Crystal Structure and Physical Properties of Yb3Co4–xRuxSn13 (x = 0, 0.38)
Authors: Schmitt Devin C. , Haldolaarachchige Neel , Young David P. , Jin Rongying , Chan Julia Y.
Published: October 2011

Single crystals of the phase Yb3Co4–xRuxSn13 (x = 0, 0.38) were grown by the flux growth method and were characterized by single crystal and powder X‐ray diffraction. Magnetic, resistivity, and thermopower measurements were performed on both doped and undoped single crystals of Yb3Co4–xRuxSn13. The Ru‐doped compound shows a sign change of the thermopower at approximately 150 K, indicating both electron and hole conductivity, as well as a complete suppression of the ytterbium magnetic moment exhibited by undopedYb3Co4Sn13. Single crystal X‐ray diffraction studies at 100 K, 298 K, and 375 K were performed, and the results are compared to published theoretical models.
Isolated distal radial metaphyseal fractures with an intact ulna: Risk factors for loss of reduction
Authors: Sankar Wudbhav N. , Beck Nicholas A. , Brewer Jordan M. , Baldwin Keith D. , Pretell Juan A.
Published: October 2011

Purpose

The purpose of this study was to determine the risk factors for loss of reduction in patients with an isolated distal radius fracture and intact ulna.

Methods

Outpatient records and initial, post-reduction, and follow-up radiographs of children with displaced distal radial metaphyseal fractures and intact ulnas that required closed reduction and casting at our institution were reviewed for demographic factors, body mass index (BMI), initial fracture displacement, residual displacement after reduction, and 3-point cast index. Loss of reduction was defined as angulation ≥15° in the coronal plane for all ages and/or angulation ≥20° in the sagittal plane for patients ≥11 years of age and ≥30° for children <11 years of age. Additionally, all patients who were remanipulated and/or pinned were considered to have lost reduction.

Results

Thirty-five of the 76 patients in our series met the criteria for loss of reduction (46%). Multivariate logistic regression revealed that initial angulation in the coronal plane and post-reduction translation in the coronal plane were independent predictors for loss of reduction. Patients with >11° of initial angulation in the coronal plane were 6.3 times as likely to lose reduction (confidence interval [CI]: 1.43–28.3, P = 0.015) and those with any amount of residual translation in the coronal plane after closed reduction were 7.8 times as likely to lose reduction (CI: 2.5–24.0, P < 0.001).

Conclusion

Our study, the largest dedicated series of distal radial metaphyseal fractures with intact ulnas, indicates that loss of reduction is common, and that risk factors include initial angulation in the coronal plane and post-reduction translation in the coronal plane.
A Brief Postwar History of U.S. Consumer Finance
Authors: Ryan Andrea , Trumbull Gunnar , Tufano Peter
Published: October 2011

In this brief history of U.S. consumer finance since World War II, the sector is defined based on the functions delivered by firms in the form of payments, savings and investing, borrowing, managing risk, and providing advice. Evidence of major trends in consumption, savings, and borrowing is drawn from time-series studies. An examination of consumer decisions, changes in regulation, and business practices identifies four major themes that characterized the consumer finance sector: innovation that increased the choices available to consumers; enhanced access in the form of consumers' broadening participation in financial activities; do-it-yourself consumer finance, which both allowed and forced consumers to take greater responsibility for their own financial lives; and a resultant increase in household risk taking.
Changes in problem-solving appraisal after cognitive therapy for the prevention of suicide
Authors: Ghahramanlou-Holloway M. , Bhar S. S. , Brown G. K. , Olsen C. , Beck A. T.
Published: October 2011

Background

Cognitive therapy has been found to be effective in decreasing the recurrence of suicide attempts. A theoretical aim of cognitive therapy is to improve problem-solving skills so that suicide no longer remains the only available option. This study examined the differential rate of change in problem-solving appraisal following suicide attempts among individuals who participated in a randomized controlled trial for the prevention of suicide.

Method

Changes in problem-solving appraisal from pre- to 6-months post-treatment in individuals with a recent suicide attempt, randomized to either cognitive therapy (n=60) or a control condition (n=60), were assessed by using the Social Problem-Solving Inventory-Revised, Short Form.

Results

Improvements in problem-solving appraisal were similarly observed for both groups within the 6-month follow-up. However, during this period, individuals assigned to the cognitive therapy condition demonstrated a significantly faster rate of improvement in negative problem orientation and impulsivity/carelessness. More specifically, individuals receiving cognitive therapy were significantly less likely to report a negative view toward life problems and impulsive/carelessness problem-solving style.

Conclusions

Cognitive therapy for the prevention of suicide provides rapid changes within 6 months on negative problem orientation and impulsivity/carelessness problem-solving style. Given that individuals are at the greatest risk for suicide within 6 months of their last suicide attempt, the current study demonstrates that a brief cognitive intervention produces a rapid rate of improvement in two important domains of problem-solving appraisal during this sensitive period.
Why should it matter that others have more? Poverty, inequality, and the potential of international human rights law
Authors: SALOMON MARGOT E.
Published: October 2011

A concern with ensuring minimum standards of dignity for all and a doctrine based on the need to secure for everyone basic levels of rights have traditionally shaped the way in which international human rights law addresses poverty. Whether this minimalist, non-relational approach befits international law objectives in the area ofworldpoverty begs consideration. This article offers three justifications as to why global material inequality – and not just poverty – should matter to international human rights law. The article then situates requirements regarding the improvement of living conditions, a system of equitable distribution in the case of hunger, and in particular obligations of international cooperation, within the post-1945 international effort at people-centred development. The contextual consideration of relevant tenets serves to demonstrate that positive international human rights law can be applied beyond efforts at poverty alleviation to accommodate a doctrine of fair global distribution.
Pluricanonical systems for 3-folds and 4-folds of general type
Authors: DI BIAGIO LORENZO
Published: October 2011

We explicitly find lower bounds on the volume of threefolds and fourfolds of general type in order to have non-vanishing of pluricanonical systems and birationality of pluricanonical maps. In the case of threefolds of large volume, we also give necessary and sufficient conditions for the fourth canonical map to be birational.
On an asymptotic formula for the maximum voltage drop in a on-chip power distribution network
Authors: AGUARELES MARIA , HARO JAUME , RIUS JOSEP , SOLÀ-MORALES J.
Published: October 2011

We present a new asymptotic formula for the maximum static voltage in a simplified model for on-chip power distribution networks of array bonded integrated circuits. In this model the voltage is the solution of the Poisson's equation in an infinite planar domain whose boundary is an array of circular pads of radius ϵ, and we deal with the singular limit ϵ → 0 case. In comparison with approximations that appear in the electronics engineering literature, our formula is more complete, since we have obtained terms up to order ϵ15. A procedure will be presented to compute all the successive terms, which can be interpreted by using multipole solutions of equations involving spatial derivatives of δ-functions. To deduce the formula, we use the method of matched asymptotic expansions. Our results are completely analytical and we make an extensive use of special functions and the Gauss constant G.
Pulsatile venous waveform quality affects the conduit performance in functional and “failing” Fontan circulations
Authors: Dur Onur , Kocyildirim Ergin , Soran Ozlem , Wearden Peter D. , Morell Victor O. , DeGroff Curt G. , Pekkan Kerem
Published: October 2011

Objective

To investigate the effect of pulsatility of venous flow waveform in the inferior and superior caval vessels on the performance of functional and “failing” Fontan patients based on two primary performance measures – the conduit power loss and the distribution of inferior caval flow (hepatic factors) to the lungs.

Methods

Doppler angiography flows were acquired from two typical extra-cardiac conduit “failing” Fontan patients, aged 13 and 25 years, with ventricle dysfunction. Using computational fluid dynamics, haemodynamic efficiencies of “failing”, functional, andin vitro-generated mechanically assisted venous flow waveforms were evaluated inside an idealised total cavopulmonary connection with a caval offset. To investigate the effect of venous pulsatility alone, cardiac output was normalised to 3 litres per minute in all cases. To quantify the pulsatile behaviour of venous flows, two new performance indices were suggested.

Results

Variations in the pulsatile content of venous waveforms altered the conduit efficiency notably. High-frequency and low-amplitude oscillations lowered the pulsatile component of the power losses in “failing” Fontan flow waveforms. Owing to the offset geometry, hepatic flow distribution depended strongly on the ratio of time-dependent caval flows and the pulsatility content rather than mixing at the junction. “Failing” Fontan flow waveforms exhibited less balanced hepatic flow distribution to lungs.

Conclusions

The haemodynamic efficiency of single-ventricle circulation depends strongly on the pulsatility of venous flow waveforms. The proposed performance indices can be calculated easily in the clinical setting in efforts to better quantify the energy efficiency of Fontan venous waveforms in pulsatile settings.