bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adaptive plasticity to heterogeneous environments increases capacity for division of labor in the clonal invader Carpobrotus edulis (Aizoaceae)
Authors: Roiloa Sergio R. , Rodriguez‐Echeverria Susana , Lopez‐Otero Aaron , Retuerto Ruben , Freitas Helena 
Published: August 2014

• Premise of the study: Clonality has been proposed as an important mechanism favoring plant invasions, but few studies have been conducted to determine the role of clonal traits on successful invaders. An interesting trait associated with clonality is the capacity for division of labor. Division of labor requires a negative spatial correlation between the availabilities of two essential resources and ramet specialization for locally abundant resources to increase the overall performance of the clone. We hypothesized that the capacity for division of labor in the clonal invader Carpobrotus edulis will be selected in those clones from patchy environments where this trait could be an advantage.• Methods: Morphological and physiological division of labor was compared between clones from coastal sand dunes (where nutrients and light show a negative spatial covariance) and from rocky coasts (where nutrients and light are homogenously distributed).• Key results: Clones from coastal sand dunes showed a greater capacity than clones from rocky coasts for division of labor. Specialization for abundance was found at the morphological (biomass allocated to roots) and the physiological (photochemical efficiency) level.• Conclusions: The greater ability for division of labor in the patchy environment where the presence of this trait would be more beneficial demonstrates the existence of local adaptation and suggests that rapid evolution in clonal traits could be contributing to the success of the invader C. edulis. This study is one of the few showing that division of labor is under selection and is the first reporting adaptive division of labor of an aggressive invader.
Miyazaki’s Little Mermaid: A Goldfish Out of Water
Authors: Ross Deborah 
Published: August 2014

Abstract
When Hayao Miyazaki’s Spirited Away reached American theaters in 2002, children by and large were enthralled, but some of us adults were confused. This English-language version of the original Japanese film bore the Disney logo, but it was clearly not Disney. It was longer, for one thing, with odd pauses during which the characters seemed to be pondering,¹ and the line between good and evil seemed blurred and shifting. On the other hand, it also did not fit the American stereotype of Japanese animation--too detailed, too expensive, and with a surprising absence of exploding robots. One thing about this movie did strike a familiar note: like many Disney features, it presented imagination as a sometimes dark and dangerous thing. That imagination is both a gift and a curse is hardly a new idea; its double-edged presence in children’s literature has long attracted scholarly attention. But for an animated film to warn viewers of the hazards of something without which it could not begin to exist seems downright hypocritical. When the most creative, surrealistic animated images are made to serve a story that preaches reason and restraint, they seem almost to erase themselves, like the path through Tulgey Wood rubbed out by broom dogs in Disney’s Alice in Wonderland (1951). Disney publicity has never officially acknowledged any ambivalence about its chief product; what would a commercial for a Disney movie or theme park be without the word "imagination" or its near relative, "dream"? Yet even the post- Walt animated films of the neoclassic period, which began in 1989 with The Little Mermaid, may convey, in the tension between their pictures and their plots, a deep sense of unease.²
Are the "Boys" at Pixar Afraid of Little Girls?
Authors: Ebrahim Haseenah 
Published: August 2014

Abstract
Christian Metz’s observation that "a film is difficult to explain because it is easy to understand" (69) appears particularly evident when one is teaching an undergraduate course on the animated feature films of Disney and Pixar. In a recent class taught in Chicago,1 many students were taken aback when they learned that the course involved historical, sociological, and theoretical framing and analysis. The students, it turned out, expected little more than discussions of the animated films’ plot events, some character and stylistic analysis, and the role of hand-drawn versus computer-generated (CG) animation in a film’s popular appeal. In addition, a refrain began to emerge--namely, "I love Disney films, but I never thought of them as being ideological." In some instances, I sensed a hint of disapproval that the course would subject Disney and Pixar to the kind of analysis that might require students to reevaluate much-loved films associated with cherished memories of childhood. I reiterated the argument I make every time I teach the course, best encapsulated by Giroux and Pollock, that the pleasures of scopophilia notwithstanding, "it is as important to comprehend and mitigate what gives us pleasure as it is to examine what elicits our disapproval" (xvi). I also make no apology for sharing those pleasures, however mitigated those may be by my own position as a film scholar (and as a parent).
Time‐lapse seismic noise correlation tomography at Valhall
Authors: de Ridder S. A. L. , Biondi B. L. , Clapp R. G. 
Published: August 2014

AbstractWe show that a reliable and statistically significant group velocity time‐lapse difference between 2004 and 2010 can be retrieved from ambient seismic noise in an offshore hydrocarbon exploitation setting. We performed a direct comparison of Scholte wave group velocity images obtained using regularized tomography. We characterize the expected variation in group velocity images from the 2004 or 2010 recordings that result from fluctuations in the cross correlations by looking at cross correlations of portions of the recordings. We prove that the time‐lapse difference is statistically significant. The time‐lapse group velocity image from ambient noise data shows strong similarities with a time‐lapse phase velocity map obtained from controlled source data. The most striking features are a northern and a southern group velocity increase due to compaction and subsidence as a result of reservoir production.
Ninety degrees pitch angle enhancements of suprathermal electrons associated with interplanetary shocks
Authors: Kajdič P. , Lavraud B. , Zaslavsky A. , Blanco‐Cano X. , Sauvaud J.‐A. , Opitz A. , Jian L. K. , Maksimovic M. , Luhmann J. G. 
Published: August 2014

AbstractWe report the results of the first systematic analysis of 90° pitch angle (PA) enhancements or the ring distributions of suprathermal (E ∼70 eV–2 keV) electrons at interplanetary (IP) shocks. We analyze 2 h time intervals around 232 IP shocks observed by the two STEREO spacecraft between 2007 and 2011. The ring distributions were detected downstream of 114 events (49%). In 52 (22.4%) cases they were detected at the shock ramp. We also found 90° enhancements upstream of 11 (4.7%) events. Statistical analysis of basic shock properties did not reveal substantial differences between the shocks that are associated with the enhancements and those that are not. The data from the STEREO/WAVES instruments revealed that the 90° PA enhancements tend to be associated with magnetic and electric field fluctuations. Although at this point we do not have a satisfactory explanation for the mechanism that produces these distributions, our findings suggest that wave‐particle interactions play a role, while pure focusing and mirroring effects due to adiabatic motion of electrons across the shock fronts cannot fully account for the observations.
Model‐data comparison of MCI field campaign atmospheric CO2 mole fractions
Authors: Díaz Isaac Liza I. , Lauvaux Thomas , Davis Kenneth J. , Miles Natasha L. , Richardson Scott J. , Jacobson Andrew R. , Andrews Arlyn E. 
Published: August 2014

AbstractAtmospheric transport model errors are a major contributor to uncertainty in CO2 inverse flux estimates. Our study compares CO2 mole fraction observations from the North American Carbon Program Mid‐Continental Intensive (MCI) field campaign and modeled mole fractions from two atmospheric transport models: the global Transport Model 5 from NOAA's CarbonTracker system and the mesoscale Weather Research and Forecasting model. Both models are coupled to identical CO2 fluxes and lateral boundary conditions from CarbonTracker (CT2009 release). Statistical analyses were performed for two periods of 2007 using observed daily daytime average mole fractions of CO2 to test the ability of these models to reproduce the observations and to infer possible causes of the discrepancies. TM5‐CT2009 overestimates midsummer planetary boundary layer CO2 for sites in the U.S. corn belt by 10 ppm. Weather Research and Forecasting (WRF)‐CT2009 estimates diverge from the observations with similar magnitudes, but the signs of the differences vary from site to site. The modeled mole fractions are highly correlated with the observed seasonal cycle (r ≥ 0.7) but less correlated in the growing season, where weather‐related changes in CO2 dominate the observed variability. Spatial correlations in residuals from TM5‐CT2009 are higher than WRF‐CT2009 perhaps due to TM5's coarse horizontal resolution and shallow vertical mixing. Vertical mixing appears to have influenced CO2 residuals from both models. TM5‐CT2009 has relatively weak vertical mixing near the surface limiting the connection between local CO2 surface fluxes and boundary layer. WRF‐CT2009 has stronger vertical mixing that may increase the connections between local surface fluxes and the boundary layer.
Eukaryotic
DNA
Polymerases
Authors: Cotterill Sue , Kearsey Stephen 
Published: August 2014

Abstract

Deoxyribonucleic acid (DNA)
is replicated and repaired by a family of enzymes called DNA polymerases. Eukaryotic cells have a diversity of these enzymes that, while sharing a common biochemical activity, are specialised for particular roles. Three polymerases are required for the replication of the nuclear genome, with Pol α involved in priming and initial synthesis and Pols δ and ϵ involved in bulk DNA replication. These polymerases are dependent on a large number of other proteins which unwind the DNA and perform other functions essential for efficient DNA synthesis. Polymerases are also involved in DNA repair and many repair‐specific enzymes have been identified. Some repair polymerases can refill a gap generated by removal of damaged DNA, or copy a damaged template, allowing DNA synthesis to proceed across a damaged template. Repair polymerases can also have tissue‐specific functions in lymphoid cells, where they contribute to somatic hypermutation of immunoglobulin genes.

Key Concepts:

Catalytic function of DNA polymerases.

Concepts of ‘proofreading’ and ‘processivity’.

Roles of replicative DNA polymerases needed for chromosome replication and organisation at the replication fork.

Function of accessory proteins needed for polymerase function in chromosome replication.

Different modes of action of specialised polymerases involved in DNA repair.

Catalytic mechanism of polymerases.

Assays used to detect polymerase function
in vitro
.

Relevance of DNA polymerases to human disease.
Cell Proliferation Assays
Authors: Yadav Kamalendra , Singhal Nitin , Rishi Vikas , Yadav Hariom 
Published: August 2014

Abstract

Cells are structural and functional unit of our body that control and maintain the function of all unicellular and multicellular organisms. The process of cell proliferation and differentiation plays a vital role from the time of embryogenesis to development of whole organism from single‐ or double‐cell embryo and continues its crucial role in maintenance of adult tissue homoeostasis by recycling the old cells with new cells. In addition, abnormal cell proliferation is also associated with various human diseases like cancer. Therefore, cell proliferation assays become crucial to scrutinise the rate of cell proliferation in both
in vitro
and
in vivo
conditions. These assays follow different parameters to determine the rate of cell proliferation like rate of
deoxyribonucleic acid
synthesis, metabolic activity of cells, different antigens associated with cell proliferation and
adenosine triphosphate
concentration. In the present article, authors have tried to summarise different cell proliferation assays commonly used in laboratories to determine cell proliferation.

Key Concepts:

Cell proliferation plays a vital role in regular tissue and cellular homoeostasis for proper growth, development and maintenance of organism.

Cell proliferation assays are mainly designed based on three concepts, that is, (1) measuring rate of DNA replication, (2) analysis of metabolic activity and (3) cell surface antigen recognitions.

Rate of DNA replication can be analysed by using radioactive or labelled nucleotide analogues, that is,
3
H‐thymidine‐ and BrdU‐based assays.

Metabolic activity‐based assays include MTT, XTT, WST, resazurin and ATP measurements.

Cell proliferation antigen‐based assay targets antigens present in proliferating cells such as markers like Ki‐67, topoisomerase IIB, phosphohistone H3 and PCNA.
Base Flipping
Authors: Cheng Xiaodong , Roberts Richard J 
Published: August 2014

Abstract

Base flipping involves rotation of backbone bonds in double‐stranded
deoxyribonucleic acid (DNA)
to expose an out‐of‐stack base, which can then be a substrate for an enzyme‐catalysed chemical reaction or for a specific protein binding interaction. The phenomenon is fully established for DNA methyltransferases, for several key DNA repair enzymes, and for a few non‐enzymatic DNA binding proteins involved in the DNA methylation and repair pathways, and is likely to prove general for enzymes or proteins that require access to unpaired, mismatched, damaged or modified bases or even undamaged and unmodified bases for specific functions. Although, detailed mechanistic information is emerging, it remains to be proven for each individual system whether base flipping is an active process in which the protein rotates the base out of the helix, or a passive one in which the protein binds to a transiently flipped base.

Key Concepts:

Base flipping is a key mechanism used by DNA and RNA modifying enzymes including DNA repair enzymes.

DNA and RNA methyltransferases use AdoMet as the methyl donor to methylate flipped nucleotides (cytosine or adenine).

The family of Fe(II)‐ and α‐ketoglutarate‐dependent dioxygenases includes members of the Tet family and AlkB‐like DNA/RNA repair enzymes.

To date, six structural superfamilies of DNA repair glycosylases and newly identified (non‐repair) sequence‐specific DNA glycosylases all use base‐flipping mechanism to access the target base.

Eukaryotic SRA domains share structural similarity to that of bacterial modification‐specific endonucleases (MspJI and AbaSI) in recognition of modified bases.

Base flipping provides a simple mechanism by which a DNA helix can be opened during the initiation of polymerisation by DNA or RNA polymerases and their associated factors.
Tandem Affinity Purification (
TAP
) Tags
Authors: Basrur Venkatesha , Lim Megan S 
Published: August 2014

Abstract

Cells respond to myriad intra‐ and extracellular cues often by modulating the formation and function of heteromeric protein complexes (PCs). Thus, developing a comprehensive picture of cellular behavior and understanding biological responses requires characterization of PCs in their proper cellular context. Tandem affinity purification (TAP) is a two‐step affinity purification method that aids in rapid isolation of PCs under native conditions. Since its original description in yeast, numerous variations of the affinity tag combinations have been developed to address some of the inadequacies of the original method and to accommodate the expanding scope of applications. The TAP, in combination with mass spectrometry, has paved the way for large‐scale characterization of PCs and the dynamic protein interaction networks (PINs) in diverse organisms over the past decade.

Key Concepts:

Characterizing the architecture of protein complexes and protein interaction networks is essential to decipher the cellular responses to environmental cues.

Sequential affinity purification steps employed in tandem‐affinity purification aid in specific and rapid purification of protein complexes.

Standardized TAP protocols could benefit both intra‐ and inter‐laboratory reproducibility of large‐scale protein complex characterization efforts.
Syndromes and Diseases Associated with the Notch Signalling Pathway
Authors: Turnpenny Peter D 
Published: August 2014

AbstractThe Notch signalling pathway refers to a highly conserved complex cell interaction mechanism, playing a crucial role in metazoan development, which eventually dictates cell fates through the implementation of differentiation, proliferation and apoptosis, ultimately influencing organ formation and morphogenesis by unlocking specific developmental programmes. In mammals, the regulation of neurogenesis, myogenesis, angiogenesis, haematopoiesis and epithelial–mesenchymal transition are all crucially influenced by Notch signalling and to date 10 genes, either core components of the pathway or signalling targets, are implicated in a diverse group of human Mendelian diseases/syndromes when mutated in the germline. These can be broadly grouped into those conditions dominated by axial skeletal defects – the spondylocostal dysostoses; those with predominantly vascular or cardiovascular abnormalities – Alagille syndrome,NOTCH1‐related congenital cardiac anomalies and CADASIL; Hajdu–Cheney syndrome, a multisystem disorder dominated by skeletal anomalies, and neurological degeneration – Alzheimer disease type 3. Notch signalling is also widely implicated in somatic genomic mutational events leading to cancer and malignancy, the best known example of which is T‐cell acute lymphoblastic leukaemia.Key Concepts:Notch signalling is a highly conserved pathway in metazoan development.The Notch gene family encodes cell surface transmembrane receptors which mediate cellular functions through direct cell–cell contact.The activation of membrane‐bound Notch results in proteolytic cleavage Notch intracellular domain (NICD), which translocates to the nucleus.The Notch intracellular domain (NICD) converts downstream targets from transcriptional repressors to transcriptional activators.Notch signalling determines cell fates in neurogenesis, myogenesis, angiogenesis, haematopoiesis and epithelial–mesenchymal transition.A key role of the Notch signalling pathway is in the developmental integrity of somitogenesis.Syndromes caused by germline mutations in Notch pathway genes include spondylocostal dysostosis, Alagille and Hajdu–Cheney.Syndromes with predominantly (cardio)vascular effects due to mutations in Notch pathway genes include congenital heart disease and CADASIL.A form of familial presenile dementia (Alzheimer disease type 3) is due to mutatedPSEN1, a Notch pathway gene.Somatic mutations in certain Notch pathway genes are increasingly being shown to contribute to various cancerous conditions.
Protein Superfamilies
Authors: Pazos Florencio , Sánchez‐Pulido Luis 
Published: August 2014

Abstract

The concept of ‘superfamily’ is key for understanding the organisation of the protein universe and extracting useful information from it. As a set of proteins with a common ancestor, a superfamily contains rich information on the structural, functional and evolutionary features of its members. It represents a good equilibrium between conservation and variability. In one hand, the members of a superfamily have the same global 3D structure, can be aligned, and share many functional aspects. On the other hand, they are variable enough to encode important information on the functional diversity of their members. This variability also allows generating informative profiles which can be used to pick up distant relatives (e.g. to predict their function or their 3D structure). For these reasons, the concept of superfamily is behind many modern approaches for studying and predicting protein function and structure. The available massive data on protein superfamilies is accessible through a number of web resources.

Key Concepts:

A superfamily is a group of protein domains arisen from a common ancestor, being such common origin evident in their sequence identities or not.

The superfamily is the most informative level of protein classification hierarchies.

The concept of superfamily is behind most methods for predicting protein structure and function.

All available information on protein superfamilies is available online in dedicated web sites.

The rate of ‘discovery’ of new superfamilies is decaying and some people think that we might be close to having ‘touched’ most superfamilies of the protein universe.
Predicting variability: Using multilevel modelling to assess differences in variance
Authors: Kuppens Toon , Yzerbyt Vincent Y. 
Published: August 2014

AbstractResearchers are sometimes interested in the variability of data rather than in their absolute or relative values. An important example of such a situation in social psychology is consensus: the fact that people are more similar to each other in certain conditions. Currently, methods to assess differences in consensus (or variability in general) are not very well‐developed or widely known. We describe an existing tool that allows testing the extent to which variability depends on one or several predictor variables. We explain how multilevel modelling's capacity to model heterogeneity in residual variance can be used to test substantive hypotheses about differences in variance. We illustrate the procedure and warn against potential misuses of multilevel modelling to analyse differences in variability. We also provide MLwiN and SAS PROC MIXED syntax necessary to run this kind of analyses. In some specific, simple cases, SPSS MIXED can also be used. Copyright © 2014 John Wiley & Sons, Ltd.
Development of haemostatic decontaminants for the treatment of wounds contaminated with chemical warfare agents. 1: Evaluation of in vitro clotting efficacy in the presence of certain contaminants
Authors: Hall Charlotte A. , Lydon Helen L. , Dalton Christopher H. , Chipman J. K. , Graham John S. , Chilcott Robert P. 
Published: August 2014

AbstractThe treatment of penetrating, haemorrhaging injuries sustained within a hazardous environment may be complicated by contamination with toxic chemicals. There are currently no specific medical countermeasures for such injuries. Haemostats with an absorbent mechanism of action have the potential to simultaneously stop bleeding and decontaminate wounds. However, a primary requirement of a ‘haemostatic decontaminant’ is the retention of clotting function in the presence of chemical contaminants. Thus, the aim of this study was to investigate the haemostatic efficacy of seven commercially available haemostats in the presence of toxic chemicals (soman, VX, sulphur mustard, petrol, aviation fuel and motor oil). Clot viscosity was assessed ex vivo using thrombelastography following treatment of pig blood with: (i) toxic chemical; (ii) haemostat; or (iii) haemostat in combination with toxic chemical. Several contaminants (VX, petrol and GD) were found to be pro‐haemostatic and none had an adverse effect on the rate with which the test products attained haemostasis. However, the total clot strength for blood treated with certain haemostats in the presence of sulphur mustard, soman and petrol was significantly decreased. Three test products failed to demonstrate haemostatic function in this ex vivo (thrombelastography) model; this was tentatively ascribed to the products achieving haemostasis through a tamponade mechanism of action, which can only be replicated using in vivo models. Overall, this study has identified a number of commercial products that may have potential as haemostatic decontaminants and warrant further investigation to establish their decontaminant efficacy. Copyright © 2014 John Wiley & Sons, Ltd.