bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractThe 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

SUMMARYThe 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.
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

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

AbstractP2X 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.24For 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

AbstractMany 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.6For 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

AbstractThe 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.112This article is categorized under:

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

AbstractPre‐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.116This 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

AbstractThe 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.163This 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

AbstractThe 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.164This 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

AbstractZirconium 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

AbstractSingle 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.
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

BackgroundCognitive 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.MethodChanges 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.ResultsImprovements 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.ConclusionsCognitive 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

AbstractA 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

AbstractWe 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.
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

AbstractObjectiveTo 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.MethodsDoppler 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.ResultsVariations 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.ConclusionsThe 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.