bluuebunny/crossref_metadata_2025_split huggingface dataset:
The crystal structure of multidrug-resistance regulator RamR with multiple drugs
Authors: Yamasaki Suguru , Nikaido Eiji , Nakashima Ryosuke , Sakurai Keisuke , Fujiwara Daisuke , Fujii Ikuo , Nishino Kunihiko 
Published: June 2013

AbstractRamR is a transcriptional repressor of the gene-encoding RamA protein, which controls the expression of the multidrug efflux system genes acrAB-tolC. RamR is an important multidrug-resistance factor, however, its structure and the identity of the molecules to which it responds have been unknown. Here, we report the crystal structure of RamR in complex with multiple drugs, including berberine, crystal violet, dequalinium, ethidium bromide and rhodamine 6G. All compounds are found to interact with Phe155 of RamR, and each compound is surrounded by different amino acid residues. Binding of these compounds to RamR reduces its DNA-binding affinity, which results in the increased expression of ramA. Our results reveal significant flexibility in the substrate-recognition region of RamR, which regulates the bacterial efflux participating in multidrug resistance.
Histone deacetylase 10 promotes autophagy-mediated cell survival
Authors: Oehme Ina , Linke Jan-Peter , Böck Barbara C. , Milde Till , Lodrini Marco , Hartenstein Bettina , Wiegand Inga , Eckert Christian , Roth Wilfried , Kool Marcel , Kaden Sylvia , Gröne Hermann-Josef , Schulte Johannes H. , Lindner Sven , Hamacher-Brady Anne , Brady Nathan R. , Deubzer Hedwig E. , Witt Olaf 
Published: June 2013

Significance
Resistance to chemotherapy is one of the major challenges in oncology. Neuroblastoma is the most common extracranial solid tumor in childhood, and the successful response of high-risk patients to chemotherapy remains poor. Our work showed that the so far poorly studied histone deacetylase (HDAC)10 promotes autophagy-mediated cell survival and signals poor outcome in independent high-risk patient cohorts. Inhibition of HDAC10 sensitized tumor cells for cytotoxic drug treatment. These results offer HDAC10 as a potential biomarker for treatment response of high-risk tumors and open new avenues for developing selective treatment strategies to bypass drug resistance of these tumors.
Industrial policy and the political settlement in Tanzania: aspects of continuity and change since independence
Authors: Gray Hazel 
Published: June 2013

This article explores Tanzania's experience of industrial policy since independence through the concept of the political settlement. Higher growth in manufacturing since 1996 has been seen as a vindication of neoliberal policies of market liberalisation. Yet, the neoliberal approach fails to take account of the important legacy of state-led industrialisation under socialism and aspects of the political economy of the state in Tanzania that explain some of the longer-term constraints on industrialisation. Critical aspects of Tanzania's political settlement relate to state–capital relations and the distribution of power between contenting factions of intermediate classes within the state.
[Politique industrielle et le règlement politique en Tanzanie: aspects de continuité et de changement depuis l'indépendance.] Cet article examine l'expérience tanzanienne en matière de politique industrielle depuis l'indépendance à travers le concept du règlement politique. La forte croissance dans le secteur industriel depuis 1996 a été considérée comme une justification de politiques néolibérales de libéralisation des marchés. Toutefois, l'approche néolibérale ne parvient pas à prendre en compte l'héritage important d'une industrialisation gérée par l'État sous le régime socialiste ainsi que les aspects de l'économie politique de l'État en Tanzanie, qui expliquent certaines des contraintes à plus long terme à l'industrialisation. Les aspects essentiels du règlement politique en Tanzanie concernent les relations État-capital et la répartition des pouvoirs entre les factions des classes intermédiaires se contentant de la situation au sein de l'État.

Mots-clés : Tanzanie; règlements politiques; politique industrielle; production industrielle; libéralisation
Labour and underdevelopment? Migration, dispossession and accumulation in West Africa and Europe
Authors: Cross Hannah 
Published: June 2013

Recent waves of accumulation have been well documented in this journal with regard to land and natural resources, but labour is missing from these important analyses of profound continuity and change. This article focuses on ‘step-wise’ migrations and specifically on cases of emigration from Senegal and entry to the Spanish labour market. The labour regime is conceptualised as unfree labour mobility, which integrates dispossession, territorial control, illegalisation, the ideology of racism and the exploitation of labour. Finding salience in earlier theories of unfree labour, this article shows how the control of capital over migration to Europe perpetuates underdevelopment.
[Travail et sous-développement? Migration, dépossession et accumulation en Afrique de l'Ouest et en Europe.] Les vagues récentes d'accumulation ont été bien documentées dans cette revue en ce qui concerne les ressources foncières et naturelles mais le travail n'est pas pris en considération dans ces analyses de continuité et de changement profonds. Cet article se concentre sur les migrations progressives et en particulier les cas d'émigration du Sénégal et d'entrée sur le marché du travail espagnol. Le régime du travail est conçu comme une mobilité du travail non-libre qui intègre la dépossession, le contrôle territorial, le travail illégal, l'idéologie du racisme et l'exploitation de la main d'œuvre. Recherchant le point saillant des théories existantes du travail non-libre, cet article montre comment le contrôle du capital sur les migrations vers l'Europe perpétue le sous-développement.

Mots-clés : mobilité de la main d'œuvre; migration; Sénégal; accumulation par dépossession; sous-développement; Europe
Using reflex action mortality predictors (RAMP) to evaluate if trawl gear modifications reduce the unobserved mortality of Tanner crab (Chionoecetes bairdi) and snow crab (C. opilio)
Authors: Hammond Carwyn F. , Conquest Loveday L. , Rose Craig S. 
Published: June 2013

Abstract
Hammond, C. F., Conquest, L. L., and Rose, C. S. 2013. Using reflex action mortality predictors (RAMP) to evaluate if trawl gear modifications reduce the unobserved mortality of Tanner crab (Chionoecetes bairdi) and snow crab (C. opilio). – ICES Journal of Marine Science, 70: . Management of Bering Sea crab and groundfish fisheries must account for the delayed (and hence unobserved) mortality of crab that encounter bottom trawls, but are not captured. A new approach to predicting the delayed mortality of crab uses a reflex action mortality predictor (RAMP) model to establish a relationship between mortality and reflex impairments. A 2007 pilot study of 649 crab established RAMP curves for both Tanner crab (Chionoecetes bairdi) and snow crab (C. opilio). Additional data (1775 crab) collected in 2008 allowed us to update the existing RAMP curves to more fully examine the effect of injury scores on the RAMP models and to determine the best method for estimating overall mortality. Results confirmed that the additional measurements did not significantly alter the original relationship between mortality and reflex impairment score. Additionally, the RAMP curves were used to predict unobserved mortality from observed reflex impairment scores of Chionoecetes spp. captured after encounters with different parts of bottom trawl gear (footrope and sweep) and alternative types of footrope and sweep. In addition to estimating mortality rates caused by each gear part, we tested whether the alternative footrope and sweep designs reduced the unobserved mortality rates of crab. Results showed that the alternative footrope (58 cm disk footrope) reduced mortality from 11.4 to 7.2% for Tanner crab and from 9.7 to 5.0% for snow crab. The alternative (off-bottom) sweep reduced mortality from 4.1 to 1.0% for Tanner crab and from 4.9 to 0.0% for snow crab. Thus, the use of the reflex impairment score through the RAMP model is a cost effective way to estimate delayed mortality and to assess the effect of gear types on delayed mortality for management purposes.
Forage fish, their fisheries, and their predators: who drives whom?
Authors: Engelhard Georg H. , Peck Myron A. , Rindorf Anna , C. Smout Sophie , van Deurs Mikael , Raab Kristina , Andersen Ken H. , Garthe Stefan , Lauerburg Rebecca A.M. , Scott Finlay , Brunel Thomas , Aarts Geert , van Kooten Tobias , Dickey-Collas Mark 
Published: June 2013

AbstractEngelhard, G. H., Peck, M. A., Rindorf, A., Smout, S. C., van Deurs, M., Raab, K., Andersen, K. H., Garthe, S., Lauerburg, R. A. M., Scott, F., Brunel, T., Aarts, G., van Kooten, T., and Dickey-Collas, M. Forage fish, their fisheries, and their predators: who drives whom? – ICES Journal of Marine Science, 71: . The North Sea has a diverse forage fish assemblage, including herring, targeted for human consumption; sandeel, sprat, and Norway pout, exploited by industrial fisheries; and some sardine and anchovy, supporting small-scale fisheries. All show large abundance fluctuations, impacting on fisheries and predators. We review field, laboratory, and modelling studies to investigate the drivers of this complex system of forage fish. Climate clearly influences forage fish productivity; however, any single-species considerations of the influence of climate might fail if strong interactions between forage fish exist, as in the North Sea. Sandeel appears to be the most important prey forage fish. Seabirds are most dependent on forage fish, due to specialized diet and distributional constraints (breeding colonies). Other than fisheries, key predators of forage fish are a few piscivorous fish species including saithe, whiting, mackerel, and horse-mackerel, exploited in turn by fisheries; seabirds and seals have a more modest impact. Size-based foodweb modelling suggests that reducing fishing mortality may not necessarily lead to larger stocks of piscivorous fish, especially if their early life stages compete with forage fish for zooplankton resources. In complex systems, changes in the impact of fisheries on forage fish may have potentially complex (and perhaps unanticipated) consequences on other commercially and/or ecologically important species.
Do terms-of-trade effects matter for trade agreements? Theory and evidence from WTO Countries*
Authors: Ludema Rodney D. , Mayda Anna Maria 
Published: June 2013

AbstractInternational trade agreements are an important element of the world economic system, but questions remain as to their purpose. The terms-of-trade hypothesis posits that countries use tariffs in part to improve their terms of trade and that trade agreements cause them to internalize the costs that such terms-of-trade shifts impose on other countries. This article investigates whether the most-favored-nation (MFN) tariffs set by World Trade Organization (WTO) members in the Uruguay Round are consistent with the terms-of-trade hypothesis. We present a model of multilateral trade negotiations featuring endogenous participation that leads the resulting tariff schedules to display terms-of-trade effects. Specifically, the model predicts that the level of the importer’s tariff resulting from negotiations should be negatively related to the product of two terms: exporter concentration, as measured by the Herfindahl-Hirschman index (sum of squared export shares), and the importer’s market power, as measured by the inverse elasticity of export supply, on a product-by-product basis. We test this hypothesis using data on tariffs, trade, and production across more than 30 WTO countries and find strong support. We estimate that the internalization of terms of trade effects through WTO negotiations has lowered the average tariff of these countries by 22% to 27% compared to its noncooperative level.
Prediction of Triticale Grain Quality Properties, Based on Both Chemical and Indirectly Measured Reference Methods, Using Near‐Infrared Spectroscopy
Authors: Manley Marena , McGoverin Cushla M. , Snyders Franci , Muller Nina , Botes Willem C. , Fox Glen P. 
Published: June 2013

ABSTRACTThe increasing demand for triticale as food, feed, and fuel has resulted in the availability of cultivars with different grain quality characteristics. Analyses of triticale composition can ensure that the most appropriate cultivars are obtained and used for the most suitable applications. Near‐infrared (NIR) spectroscopy is often used for rapid measurements during quality control and has consequently been investigated as a method for the measurement of protein, moisture, and ash contents, as well as kernel hardness (particle size index [PSI]) and sodium dodecyl sulfate (SDS) sedimentation from both whole grain and ground triticale samples. NIR spectroscopy prediction models calculated using ground samples were generally superior to whole grain models. Protein content was the most effectively modeled quality property; the best ground grain calibration had a ratio of the standard error of test set validation to the standard deviation of the reference data of the test set (RPDtest) of 4.81, standard error of prediction (SEP) of 0.52% (w/w), and r2 of 0.95. Whole grain protein calibrations were less accurate, with optimum RPDtest of 3.54, SEP of 0.67% (w/w), and r2 of 0.92. NIR spectroscopy calibrations based on direct chemical reference measurements (protein and moisture contents) were better than those based on indirect measurements (PSI, ash content, and SDS sedimentation). Calibrations based on indirect measurements would, however, still be useful to identify extreme samples.
Effects of Roll Gap, Kernel Shape, and Moisture on Wheat Breakage Modeled Using the Double Normalized Kumaraswamy Breakage Function
Authors: Fuh Kenneth F. , Coate Joanna M. , Campbell Grant M. 
Published: June 2013

ABSTRACTFlour milling separates endosperm from bran through repeated roller milling and sifting, in which the size distribution of particles produced by the initial breakage of the wheat kernels critically affects the process. The double normalized Kumaraswamy breakage function (DNKBF), previously developed to describe wheat breakage during roller milling, was extended to refine the modeling of the effect of roll gap on breakage. The DNKBF describes two populations of particles arising from roller milling of wheat, a narrow peak of mid‐sized particles and a wider distribution of both small and very large particles. A new dataset was obtained from milling a set of wheat samples bred to give a range of shapes by cross‐breeding a conventional wheat, Cappelle, with an almost spherical wheat, Triticum sphaerococcum. A residual analysis showed a statistically significant effect of kernel shape on breakage using this new dataset. This analysis supports earlier suggestions that more elongated kernels break to give slightly larger particles than more spherical kernels of equivalent hardness, because of the relatively greater bran content of elongated kernels. The extended DNKBF was also used to model effects of moisture content, showing a distinct disjunction at around 16% moisture that aligns with commercial practice for wheat milling.
Rice Grain Morphological Characteristics Correlate with Grain Weight and Milling Quality
Authors: Xie Lihong , Tang Shaoqing , Chen Neng , Luo Ju , Jiao Guiai , Shao Gaoneng , Wei Xiangjin , Hu Peisong 
Published: June 2013

ABSTRACTUsing image analysis technology, the morphological measurements of paddy, brown (BR), and milled (MR) grains of 408 rice (Oryza sativa L.) lines representing a wide range of grain morphology were obtained, and the measurements' relationships with grain weight, milling quality, and chalkiness were investigated. The principal component analysis identified two morphological traits with a total variance of 95.7% in MR. Weight of MR was modeled as a function of the principal components using linear regression (R2 = 0.95). For milling quality measurements, dominance analyses indicated that single grain weight of the paddy and BR grains were two primary parameters in determination of BR and MR recovery, whereas surface area, perimeter, and diameter were primary parameters that controlled head milled rice (HR) recovery. All measured morphological properties (surface area, perimeter, diameter, length, width, length‐to‐width ratio, roundness, and thickness) and grain weight significantly correlated with percentage of chalky (%C) grain and chalkiness (%C × % area with chalk) for all milled grains. The grain width, roundness, and thickness positively correlated with chalkiness, whereas the length and length‐to‐width ratio negatively correlated with chalkiness. The growing environment significantly affected grain HR recovery, %C grain, and chalkiness but had little effect on grain morphology and weight.
First Report of the Armillaria Root Disease Pathogen, Armillaria gallica, on Douglas-fir (Pseudotsuga menziesii) in Arizona
Authors: Nelson E. V. , Fairweather M. L. , Ashiglar S. M. , Hanna J. W. , Klopfenstein N. B. 
Published: June 2013

In August 2010, a mycelial fan (isolate AZ32F) of Armillaria sp. was collected from the root collar of a living Douglas-fir tree on the Mogollon Rim within the Coconino National Forest (approximate location 34°25′31.26″N, 111°20′41.04″W, elevation 2,293 m) in central Arizona. Mycelial fans under the bark of living trees are a sign of pathogenicity, and symptoms of the diseased tree included resinosis, sloughing bark, and thinning crown. The infected tree was located on a south-facing slope with approximately 30% tree cover, dominated by ponderosa pine (Pinus ponderosa), with lesser components of Douglas-fir and Gambel oak (Quercus gambelii). Based on three replications of somatic incompatibility tests against 24 tester isolates representing seven North American Armillaria spp., isolate AZ32F showed 100% intraspecific compatibility (colorless antagonism) with all four A. gallica isolates, 22% compatibility with A. calvescens, and 0% compatibility with the remaining Armillaria spp. Based on GenBank BLASTn of isolate AZ32F sequences, the partial LSU-IGS1 (GenBank Accession No. KF186682) showed 99 to 100% similarity to A. gallica and two other related Armillaria spp. with 99 to 100% coverage, and translation elongation factor-1 alpha (tef-1α) sequences (KC525954) showed 96% similarity to A. gallica (JF895844) with 100% coverage. Thus, isolate AZ32F was identified as A. gallica, based on somatic incompatibility tests and DNA sequences (partial LSU-IGS1 and tef-1α). Although the isolate is identified as A. gallica with similarities to other North American isolates, evidence is mounting that currently recognized A. gallica likely represents a species complex that comprises multiple phylogenetic species (4). Previous surveys in Arizona have noted A. mellea and A. solidipes (as A. ostoyae) (3), but A. gallica has never been previously confirmed in this state. Within North America, A. gallica is commonly reported east of the Rocky Mountains and in West Coast states of the United States, where it infects hardwoods and conifers including Douglas-fir (1,2). Its ecological behavior ranges from saprophyte to weak/aggressive pathogen (1,2). Because damage by A. gallica appears to increase on hosts predisposed by stress (1), further surveys are needed to document its distribution, frequency, and ecological behavior in the southwestern United States, where climate change will likely cause tree stress due to maladaptation. Continued surveys for Armillaria spp. will better determine their potential threat within the geologically and ecologically unique Mogollon Rim of Arizona. References: (1) K. Baumgartner and D. M. Rizzo. Plant Dis. 85:947, 2001. (2) N. J. Brazee and R. L. Wick. For. Ecol. Manage. 258:1605, 2009. (3) R. L. Gilbertson and D. M. Bigelow. J. Arizona-Nevada Acad. Sci. 31:13, 1998. (4) M.-S. Kim et al. Phytopathology 102:S4.63, 2012.
The body beyond the body: expectation of a sensory event is enough to induce ownership over a fake hand
Authors: Ferri Francesca , Chiarelli Antonio Maria , Merla Arcangelo , Gallese Vittorio , Costantini Marcello 
Published: June 2013

More than 100 papers have been published on the rubber hand illusion since its discovery 14 years ago. The illusion has been proposed as a demonstration that the body is distinguished from other objects by its participation in specific forms of intermodal perceptual correlation. Here, we radically challenge this view by claiming that perceptual correlation is not necessary to produce the experience of this body as mine. Each of 15 participants was seated with his/her right arm resting upon a table just below another smaller table. Thus, the real hand was hidden from the participant's view and a life-sized rubber model of a right hand was placed on the small table in front of the participant. The participant observed the experimenter's hand while approaching—without touching—the rubber hand. Phenomenology of the illusion was measured by means of skin conductance response and questionnaire. Both measures indicated that participants experienced the illusion that the experimenter's hand was about to touch their hidden hand rather than the rubber hand, as if the latter replaced their own hand. This did not occur when the rubber hand was rotated by 180° or replaced by a piece of wood. This illusion indicates that our brain does not build a sense of self in a merely reactive way, via perceptual correlations; rather it generates predictions on what may or may not belong to itself.
An Improved Simplified High-Sensitivity Quantification Method for Determining Brassinosteroids in Different Tissues of Rice and Arabidopsis
Authors: Xin Peiyong , Yan Jijun , Fan Jinshi , Chu Jinfang , Yan Cunyu 
Published: June 2013

Abstract
Quantification of brassinosteroids is essential and extremely important to study the molecular mechanisms of their physiological roles in plant growth and development. Herein, we present a simple, material and cost-saving high-performance method for determining endogenous brassinosteroids (BRs) in model plants. This new method enables simultaneous enrichment of a wide range of bioactive BRs such as brassinolide, castasterone, teasterone, and typhasterol with ion exchange solid-phase extraction and high-sensitivity quantitation of these BRs based on isotope dilution combined with internal standard approach. For routine analysis, the consumption of plant materials was reduced to one-twentieth of previously reported and the overall process could be completed within 1 day compared with previous 3 to 4 days. The strategy was validated by profiling BRs in different ecotypes and mutants of rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana), and the BR distributions in different model plants tissues were determined with the new method. The method allows plant physiologists to monitor the dynamics and distributions of BRs with 1 gram fresh weight of model plant tissues, which will speed up the process for the molecular mechanism research of BRs with these model plants in future work.