bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methods for Expressing and Analyzing GFP-Tubulin and GFP-Microtubule-Associated Proteins
Authors: Goodson Holly V. , Dzurisin Jill S. , Wadsworth Patricia 
Published: September 2010

INTRODUCTIONImportant advances in our understanding of the organization and dynamics of the cytoskeleton have been made by direct observations of fluorescently tagged cytoskeletal proteins in living cells. In early experiments, the cytoskeletal protein of interest was purified, covalently modified with a fluorescent dye, and microinjected into living cells. In the mid-1990s, a powerful new technology arose: Researchers developed methods for expressing chimeric proteins consisting of the gene of interest fused to green fluorescent protein (GFP). This approach has become a standard method for characterizing protein localization and dynamics. More recently, a profusion of “XFP” (spectral variants of GFP) has been developed, allowing researchers straightforwardly to perform experiments ranging from simultaneous co-observation of protein dynamics to fluorescence recovery after photobleaching (FRAP), fluorescence resonance energy transfer (FRET), and subresolution techniques such as stimulated emission-depletion microscopy (STED) and photoactivated localization microscopy (PALM). In this article, the methods used to express and analyze GFP- and/or XFP-tagged tubulin and microtubule-associated proteins (MAPs) are discussed. Although some details may be system-specific, the methods and considerations outlined here can be adapted to a wide variety of proteins and organisms.
ArabidopsisVILLIN1 and VILLIN3 Have Overlapping and Distinct Activities in Actin Bundle Formation and Turnover
Authors: Khurana Parul , Henty Jessica L. , Huang Shanjin , Staiger Andrew M. , Blanchoin Laurent , Staiger Christopher J. 
Published: September 2010

AbstractActin filament bundles are higher-order cytoskeletal structures that are crucial for the maintenance of cellular architecture and cell expansion. They are generated from individual actin filaments by the actions of bundling proteins like fimbrins, LIMs, and villins. However, the molecular mechanisms of dynamic bundle formation and turnover are largely unknown. Villins belong to the villin/gelsolin/fragmin superfamily and comprise at least five isovariants in Arabidopsis thaliana. Different combinations of villin isovariants are coexpressed in various tissues and cells. It is not clear whether these isovariants function together and act redundantly or whether they have unique activities. VILLIN1 (VLN1) is a simple filament-bundling protein and is Ca2+ insensitive. Based on phylogenetic analyses and conservation of Ca2+ binding sites, we predict that VLN3 is a Ca2+-regulated villin capable of severing actin filaments and contributing to bundle turnover. The bundling activity of both isovariants was observed directly with time-lapse imaging and total internal reflection fluorescence (TIRF) microscopy in vitro, and the mechanism mimics the “catch and zipper” action observed in vivo. Using time-lapse TIRF microscopy, we observed and quantified the severing of individual actin filaments by VLN3 at physiological calcium concentrations. Moreover, VLN3 can sever actin filament bundles in the presence of VLN1 when calcium is elevated to micromolar levels. Collectively, these results demonstrate that two villin isovariants have overlapping and distinct activities.
Potential consequences of replacing a retail alcohol monopoly with a private licence system: results from Sweden
Authors: Norström Thor , Miller Ted , Holder Harold , Österberg Esa , Ramstedt Mats , Rossow Ingeborg , Stockwell Tim 
Published: September 2010

ABSTRACTAim To examine the potential effects of replacing the Swedish alcohol retail system with a private licensing system on alcohol consumption and alcohol‐related harm.Design Two possible scenarios were analysed: (1) replacing the current alcohol retail monopoly with private licensed stores that specialize in alcohol sales or (2) making all alcohol available in grocery stores. We utilized a multiplicative model that projected effects of changes in a set of key factors including hours of sale, retail prices, promotion and advertising and outlet density. Next, we estimated the effect of the projected consumption increase on a set of harm indicators. Values for the model parameters were obtained from the research literature.Measurements Measures of alcohol‐related harm included explicitly alcohol‐related mortality, accident mortality, suicide, homicide, assaults, drinking driving and sickness absence.Findings According to the projections, scenario 1 yields a consumption increase of 17% (1.4 litres/capita), which in turn would cause an additional 770 deaths, 8500 assaults, 2700 drinking driving offences and 4.5 million sick days per year. The corresponding figures for scenario 2 are a consumption increase of 37.4% (3.1 litres/capita) leading to an additional annual toll of 2000 deaths, 20 000 assaults, 6600 drinking driving offences and 11.1 million days of sick leave.Conclusions Projections based on the research literature suggest that privatization of the Swedish alcohol retail market would significantly increase alcohol consumption and alcohol‐related harm.
Centrally necrotizing carcinoma of the breast: clinicopathological analysis of 33 cases indicating its basal‐like phenotype and poor prognosis
Authors: Yu Lin , Yang Wentao , Cai Xu , Shi Daren , Fan Yuezhen , Lu Hongfen 
Published: September 2010

Yu L, Yang W, Cai X, Shi D, Fan Y & Lu H (2010) Histopathology 57, 193–201 Centrally necrotizing carcinoma of the breast: clinicopathological analysis of 33 cases indicating its basal‐like phenotype and poor prognosis Aims:  To investigate the clinicopathological features and immunophenotype of centrally necrotizing carcinoma (CNC) of the breast to ascertain its relationship to basal‐like phenotype and its prognosis.Methods and results:  The clinical and pathological characteristics of 33 CNCs were reviewed. Immunohis‐tochemical study of oestrogen receptor, progesterone receptor, HER2, cytokeratin (CK) 8/18, high‐molecular‐weight CK (34βE12), CK5/6, CK14, CK17, smooth muscle antigen, p63, vimentin and epidermal growth factor receptor was performed. The striking feature of CNC was a central, necrotic or acellular zone surrounded by a ring‐like area of viable tumour cells. The central zone showed three morphological types: predominance of coagulative necrosis (21 cases), predominance of fibrosis and scar tissue (nine cases) and infarction (three cases). Tumour cells displayed invasive ductal carcinoma of high grade. The expression rate of basal‐like markers was higher than that of myoepithelial markers (87.9% versus 46.2%). Basal‐like subtype was shown by 63.6% of cases. The expression rate of CK5/6 (90.5%) was highest among basal‐like markers. Follow‐up data of 19 patients were available. Median progression‐free survival was 15.5 months. In 12 patients (63.2%), local recurrence and/or distant metastasis developed (median time to recurrence and/or metastasis, 14.0 months).Conclusions:  CNC has distinctive morphological features, which mostly exhibit a basal‐like immunophenotype and poor prognosis. CNC is a typical representative of basal‐like breast cancer.
Drought limitation of photosynthesis differs between C3 and C4 grass species in a comparative experiment
Authors: TAYLOR S. H. , RIPLEY B. S. , WOODWARD F. I. , OSBORNE C. P. 
Published: September 2010

ABSTRACTPhylogenetic analyses show that C4 grasses typically occupy drier habitats than their C3 relatives, but recent experiments comparing the physiology of closely related C3 and C4 species have shown that advantages of C4 photosynthesis can be lost under drought. We tested the generality of these paradoxical findings in grass species representing the known evolutionary diversity of C4 NADP‐me and C3 photosynthetic types. Our experiment investigated the effects of drought on leaf photosynthesis, water potential, nitrogen, chlorophyll content and mortality. C4 grasses in control treatments were characterized by higher CO2 assimilation rates and water potential, but lower stomatal conductance and nitrogen content. Under drought, stomatal conductance declined more dramatically in C3 than C4 species, and photosynthetic water‐use and nitrogen‐use efficiency advantages held by C4 species under control conditions were each diminished by 40%. Leaf mortality was slightly higher in C4 than C3 grasses, but leaf condition under drought otherwise showed no dependence on photosynthetic‐type. This phylogenetically controlled experiment suggested that a drought‐induced reduction in the photosynthetic performance advantages of C4 NADP‐me relative to C3 grasses is a general phenomenon.
Does Social Mating System Influence Nest Defence Behaviour in Great Reed Warbler (Acrocephalus arundinaceus) Males?
Authors: Trnka Alfréd , Prokop Pavol 
Published: September 2010

AbstractIn birds with biparental care, males and females often conflict over how much care to provide to their offspring and it may be substantially influenced by increased level of polygamy. In accordance with sexual conflict theory, males of socially polygynous bird species provide much less care to their nestlings than do males of most socially monogamous species. Most of previous studies, however, have used feeding behaviour as an index for variations in male parental care only. However, this may be skewed if polygynous males compensate for lower feeding assistance through the provision of other parental care such as protection of nests from predators. In this paper, we examine nest defence behaviour in the facultatively polygynous great reed warbler with respect to sex and type of social mating system. We recorded latency to the first arrival, distance from the predator and defensive reaction of each parent towards a human intruder. Socially polygynous males with two simultaneously active nests defended primary females’ nests less vigorously than socially monogamous males, whereas no differences were found between monogamous and primary females. Generally, however, they took a bigger role in nest defence than males in all cases. Our results support an idea that sexual conflict is driven by polygamy and that type of social mating system can influence nest defence behaviour of facultatively polygynous birds. This finding should be taken into consideration when studying nest defence parental care in polygynous mating systems.
Ideational Origins of Progressive Judicial Activism: The Colombian Constitutional Court and the Right to Health
Authors: Nunes Rodrigo M. 
Published: September 2010

Abstract
Why do some constitutional transitions trigger the emergence of progressive judicial activism? This article addresses this question through an analysis of the creation of the Colombian Constitutional Court and its subsequent activism toward rights in general and the right to health in particular. This research suggests that ideational variables are crucial to explain this outcome. On the one hand, the Constitutional Court's behavior reflects the dominance of the institutional conception that it is the judiciary's role to help fulfill the promises of the constitutional text. On the other, programmatic beliefs about the relationship between the rule of law and market-driven economic growth led powerholders to create the court and appoint judges with this orientation. The emergence of progressive judicial activism in Colombia, this analysis suggests, was the unexpected outcome of purposeful political choices made by proponents of neoliberal economics.
Nickel on the Swedish market: follow‐up 10 years after entry into force of the EU Nickel Directive
Authors: Biesterbos Jacqueline , Yazar Kerem , Lidén Carola 
Published: September 2010

Background. The EU Nickel Directive, aimed at primary and secondary prevention of nickel allergy by limitation of nickel release from certain items, came fully into force in July 2001. Objectives. To assess the prevalence on the market of items with nickel release and to compare the outcome with previous studies performed in Sweden in 1999 and 2002–2003. Materials and Methods. Nickel release from 659 items covered by the EU Nickel Directive was assessed with the dimethylglyoxime (DMG) test. Special attention, as compared with the previous surveys, was given to cheap jewellery in street markets and sewing materials in haberdashery shops. Results. Nickel release was shown for 9% of the tested items, all of which were intended for direct and prolonged contact with the skin. A high proportion of items bought at haberdashery shops and street markets, 34% and 61%, respectively, showed nickel release. Conclusions. The Swedish market for products intended for direct and prolonged contact with the skin has largely adapted to the Nickel Directive. It is suggested that authorities should monitor the market regularly and give attention to areas where compliance with the requirements is poor, for protection of public health.
Deregulated Semantic Cognition Follows Prefrontal and Temporo-parietal Damage: Evidence from the Impact of Task Constraint on Nonverbal Object Use
Authors: Corbett Faye , Jefferies Elizabeth , Lambon Ralph Matthew A. 
Published: September 2010

Abstract
Semantic cognition, which encompasses all conceptually based behavior, is dependent on the successful interaction of two key components: conceptual representations and regulatory control. Qualitatively distinct disorders of semantic knowledge follow damage to the different parts of this system. Previous studies have shown that patients with multimodal semantic impairment following CVA—a condition referred to as semantic aphasia (SA)—perform poorly on a range of conceptual tasks due to a failure of executive control following prefrontal and/or temporo-parietal infarction [Jefferies, E., & Lambon Ralph, M. A. Semantic impairment in stroke aphasia versus semantic dementia: A case-series comparison. Brain, 129, 2132–2147, 2006]. Although a deficit of core semantic control would be expected to impair all modalities in parallel, most research exploring this condition has focused on tasks in the verbal domain. In a novel exploration of semantic control in the nonverbal domain, therefore, we assessed eight patients with SA on two experiments that examined object use knowledge under different levels of task constraint. Patients exhibited three key characteristics of semantic deregulation: (a) difficulty using conceptual knowledge flexibly to support the noncanonical uses of everyday objects; (b) poor inhibition of semantically related distractor items; and (c) improved object use with the provision of more tightly constraining task conditions following verbal and pictorial cues. Our findings are consistent with the notion that a neural network incorporating the left inferior prefrontal and temporo-parietal areas (damaged in SA) underpins regulation of semantic activation across both verbal and nonverbal modalities.
African signatures of recent positive selection in human FOXI1
Authors: Moreno-Estrada Andrés , Aparicio-Prat Estel , Sikora Martin , Engelken Johannes , Ramírez-Soriano Anna , Calafell Francesc , Bosch Elena 
Published: September 2010

Abstract

Background
The human FOXI1 gene codes for a transcription factor involved in the physiology of the inner ear, testis, and kidney. Using three interspecies comparisons, it has been suggested that this may be a gene under human-specific selection. We sought to confirm this finding by using an extended set of orthologous sequences. Additionally, we explored for signals of natural selection within humans by sequencing the gene in 20 Europeans, 20 East Asians and 20 Yorubas and by analysing SNP variation in a 2 Mb region centered on FOXI1 in 39 worldwide human populations from the HGDP-CEPH diversity panel.

Results
The genome sequences recently available from other primate and non-primate species showed that FOXI1 divergence patterns are compatible with neutral evolution. Sequence-based neutrality tests were not significant in Europeans, East Asians or Yorubas. However, the Long Range Haplotype (LRH) test, as well as the iHS and XP-Rsb statistics revealed significantly extended tracks of homozygosity around FOXI1 in Africa, suggesting a recent episode of positive selection acting on this gene. A functionally relevant SNP, as well as several SNPs either on the putatively selected core haplotypes or with significant iHS or XP-Rsb values, displayed allele frequencies strongly correlated with the absolute geographical latitude of the populations sampled.

Conclusions
We present evidence for recent positive selection in the FOXI1 gene region in Africa. Climate might be related to this recent adaptive event in humans. Of the multiple functions of FOXI1, its role in kidney-mediated water-electrolyte homeostasis is the most obvious candidate for explaining a climate-related adaptation.
Genetic divergence of influenza A NS1 gene in pandemic 2009 H1N1 isolates with respect to H1N1 and H3N2 isolates from previous seasonal epidemics
Authors: Campanini Giulia , Piralla Antonio , Paolucci Stefania , Rovida Francesca , Percivalle Elena , Maga Giovanni , Baldanti Fausto 
Published: September 2010

Abstract

Background
The Influenza A pandemic sustained by a new H1N1 variant (H1N1v) started in Mexico and the USA at the end of April 2009 spreading worldwide in a few weeks. In this study we investigate the variability of the NS1 gene of the pandemic H1N1v strain with respect to previous seasonal strains circulating in humans and the potential selection of virus variants through isolation in cell culture.

Methods
During the period April 27th 2009-Jan 15th 2010, 1633 potential 2009 H1N1v cases have been screened at our center using the CDC detection and typing realtime RT-PCR assays. Virus isolation on MDCK cells was systematically performed in 1/10 positive cases. A subset of 51 H1N1v strains isolated in the period May-September 2009 was selected for NS1 gene sequencing. In addition, 15 H1N1 and 47 H3N2 virus isolates from three previous seasonal epidemics (2006-2009) were analyzed in parallel.

Results
A low variability in the NS1 amino acid (aa) sequence among H1N1v isolates was shown (aa identity 99.5%). A slightly higher NS1 variability was observed among H1N1 and H3N2 strains from previous epidemics (aa identity 98.6% and 98.9%, respectively). The H1N1v strains were closely related (aa identity 92.1%) to swine reference strain (A/swine/Oklahoma/042169/2008). In contrast, substantial divergence (aa identity 83.4%) with respect to human reference strain A/Brevig Mission/1/1918 and previous epidemic strains H1N1 and H3N2 (aa identity 78.9% and 77.6%, respectively) was shown. Specific sequence signatures of uncertain significance in the new virus variant were a C-terminus deletion and a T215P substitution.

Conclusions
The H1N1v NS1 gene was more conserved than that of previous epidemic strains. In addition, a closer genetic identity of H1N1v with the swine than the human reference strains was shown. Hot-spots were shown in the H1N1v NS1 aa sequence whose biologic relevance remains to be investigated.
Galactoglucomannan stabilization during the initial kraft cooking of Scots pine
Authors: Paananen Markus , Tamminen Tarja , Nieminen Kaarlo , Sixta Herbert 
Published: September 2010

Abstract
The behaviour of wood components was studied during kraft cooking of Wiley milled Scots pine (Pinus sylvestris L.) at low temperatures characteristic for the initial phase, but comprising alkali concentrations ranging from 0.31 mol l-1 to 1.55 mol l-1. The results confirmed the extensive dissolution/degradation rate of galactoglucomannan (GGM) already in the beginning of a kraft cook applying standard conditions. More than 70% of GGM was eliminated along with lignin removal of approximately 30%. A relatively high GGM yield increase of almost 2.5% on o.d. (oven dry) wood has been observed when both the temperature and the alkali concentration was raised to 130°C and to approximately 1.5 mol l-1, respectively, suggesting that stopping reactions were favoured over peeling reactions. Parallel to the pronounced stabilization of GGM, arabinoxylan experienced an additional loss of approximately 0.5–0.7% on o.d. wood, presumably owing to dissolution rather than alkaline degradation. A comprehensive kinetic model describing the alkaline degradation of GGM along with the lignin removal has been developed based on Wiley milled Scots pine raw material. The proposed kinetic model combines the alkali-dependent equilibria between ionized species of carbohydrate components with the time-dependent rate expressions of peeling, stopping, and alkaline hydrolysis. The model successfully describes the removal of GGM and lignin during initial kraft cooking. The kinetic expressions for the alkaline hydrolysis of carbohydrates were, however, less reliable owing to the limitation of the experiments to low temperatures only.
Applying digital image correlation to wood strands: Influence of loading rate and specimen thickness
Authors: Jeong Gi Young , Zink-Sharp Audrey , Hindman Daniel P. 
Published: September 2010

Abstract
Previous studies were devoted to various applications of digital image correlation (DIC) to wood and wood-based composites. However, the focus of these studies was qualitative strain distribution. Overall, there is a lack of testing protocols of DIC for quantifying the elastic properties of woody materials. The objective of this study was to investigate the effects of different specimen thicknesses and loading rates on measurement of Young's modulus and Poisson's ratio by DIC. Young's modulus from DIC decreased as thickness increased at a loading rate of 0.254 mm min-1. Comparing the different loading rates at a thickness of 0.794 mm, Young's modulus from DIC was not in agreement with the value obtained by means of the extensometer regardless of loading rate. However, Young's modulus from DIC at a thickness of 0.381 mm and a loading rate of 0.254 mm min-1 was in good agreement with the corresponding Young's modulus obtained by an extensometer. Poisson's ratio measured from different loading rates and specimen thicknesses was not significantly different between the two measurement systems. From the testing arrangement applied for this study, it is recommended that DIC should be applied at a loading rate of 0.254 mm min-1 or slower for strands with a thickness of 0.381 mm or less.