bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lytic immune synapse function requires filamentous actin deconstruction by Coronin 1A
Authors: Mace Emily M. , Orange Jordan S. 
Published: April 2014

SignificanceNatural killer (NK) cells are cytolytic effector cells of the innate immune system. They are critical for the control of viral infection and malignancy, and patients with impaired NK cell function have recurrent and often fatal viral infection and malignancy. NK cell cytotoxic function is exerted by secretion of specialized lytic granules. Here, we show that deconstruction of synaptic cortical filamentous (F)-actin by Coronin 1A (Coro1A) is required for NK cell cytotoxicity through the remodeling of F-actin to enable lytic granule secretion. We define this requirement for remodeling using superresolution nanoscopy and Coro1A-deficient NK cells. In addition, we use NK cells from a patient with a rare Coro1A mutation, thus illustrating a critical link between Coro1A function and human health.
Natural insertions in rice commonly form tandem duplications indicative of patch-mediated double-strand break induction and repair
Authors: Vaughn Justin N. , Bennetzen Jeffrey L. 
Published: April 2014

Significance
Very short insertions are usually attributable to replication slippage. Another class of longer insertions (>10 bp) creates tandem duplications even in the absence of preexisting repeats. This work provides analysis into the properties and mechanistic implications of such insertion polymorphisms segregating in rice. To our knowledge, this work is the first comprehensive analysis of this major class of natural mutations in any plant. Inspired by the prior experiments of Stéphane Vispé and Masahiko Satoh, we propose a model for how a substantial number of double-strand breaks are created and how they might result in tandem duplications. The model, based on patch-mediated nick repair, is indirectly supported by recently published experiments using a modified CRISPR-associated 9 nicking enzyme.
A bottom-up control on fresh-bedrock topography under landscapes
Authors: Rempe Daniella M. , Dietrich William E. 
Published: April 2014

SignificanceHilly landscapes are typically mantled with soil and underlain by a weathered bedrock zone that may extend tens of meters beneath the surface before reaching fresh bedrock. The weathered bedrock zone influences water runoff to channels, the chemistry of that water, the rates and processes of erosion, and atmospheric processes due to plant uptake of moisture and return to the atmosphere. However, the spatial pattern of the underlying fresh-bedrock surface is essentially unknown. We present a testable model that predicts hillslope form and the depth to fresh bedrock. The depth increases upslope and depends strongly on the porosity and permeability of the bedrock and the rate of channel incision at the base of the hillslope.
Importance of Understanding Landscape Biases in USGS Gage Locations: Implications and Solutions for Managers
Authors: Deweber Jefferson Tyrell , Tsang Yin-Phan , Krueger Damon M , Whittier Joanna B , Wagner Tyler , Infante Dana M , Whelan Gary 
Published: April 2014

ABSTRACT
Flow and water temperature are fundamental properties of stream ecosystems upon which many freshwater resource management decisions are based. U.S. Geological Survey (USGS) gages are the most important source of streamflow and water temperature data available nationwide, but the degree to which gages represent landscape attributes of the larger population of streams has not been thoroughly evaluated. We identified substantial biases for seven landscape attributes in one or more regions across the conterminous United States. Streams with small watersheds (&lt;10 km2) and at high elevations were often underrepresented, and biases were greater for water temperature gages and in arid regions. Biases can fundamentally alter management decisions and at a minimum this potential for error must be acknowledged accurately and transparently. We highlight three strategies that seek to reduce bias or limit errors arising from bias and illustrate how one strategy, supplementing USGS data, can greatly reduce bias.
RESUMEN
la temperatura y flujo de agua son propiedades fundamentales de los ecosistemas fluviales, sobre los cuales se toman diversas decisiones de manejo en cuanto a recursos dulceacuícolos. Los sensores del Estudio Geológico de los Estados Unidos de Norte América (EGEU) son la fuente disponible más importante de datos de flujo de agua y temperatura a nivel nacional, pero el grado al cual los sensores son representativos de los atributos paisajísticos de una población más grande de ríos, no ha sido analizado a profundidad. Se identificaron sesgos sustanciales en siete atributos paisajísticos en una o más regiones a lo largo de las zonas limítrofes de los Estados Unidos de Norte América. Los ríos de cauce pequeño (&lt;10 km2) y aquellos localizados en regiones elevadas no estuvieron adecuadamente representados, y los mayores sesgos se observaron en los sensores que miden la temperatura del agua y en las regiones áridas. Los sesgos tienen el potencial de alterar de manera fundamental las decisiones de manejo, y como mínimo este error tiene que reconocerse de forma precisa y transparente. Se plantean tres estrategias que buscan tanto reducir el sesgo o limitar los errores que surgen de dicho sesgo, como ilustrar cómo una estrategia, suplementando los datos EGEU, puede reducir el sesgo de manera importante.
Validating and Improving Life History Data in FishBase
Authors: Patrick Wesley S , Cope Jason M , Thorson James T 
Published: April 2014

ABSTRACT
Life history parameters of fish stocks are central to ecological research and management, including the fields of macro-ecology, fisheries science, and ecosystem modeling. The need for such information has led to several life history databases being developed to support and disseminate this information publicly. However, there has been little independent evaluation of the precision and accuracy of the life history values in these databases. This article summarizes a recent evaluation of FishBase, one of the largest and oldest life history databases, by distinguishing biases among seven life history parameters, two types of information available in FishBase (i.e., Entered vs. Generated data), and two taxa (i.e., Teleost vs. Chondrichthyan). In general, the study shows that certain types of information like data “entered” by experts are relatively accurate and precise, while empirically “generated” were not. We conclude with some ideas on how American Fisheries Society members can improve upon the data already available within FishBase.
RESUMEN
los parámetros de la historia de vida de los stocks de peces son parte fundamental de la investigación ecológica y del manejo, lo que incluye a disciplinas como la macroecología, la ciencia pesquera y la modelación ecológica. La necesidad de conocer estos aspectos ha impulsado la creación y desarrollo de distintas bases de datos de historia de vida con el fin de mantener y difundir públicamente esta información. Sin embargo, ha habido pocas evaluaciones de carácter independiente acerca de la precisión y exactitud de los valores de historia de vida en dichas bases. En este artículo se sintetiza una evaluación hecha recientemente a FishBase, una de las bases de datos más grande y antigua de historias de vida, en la que se hizo una distinción de sesgos entre siete parámetros de historia de vida, entre dos tipos de información disponible en FishBase (i.e. capturada vs. datos generados) y entre dos taxa (i.e. teleósteos vs. condrictios). En general, el estudio muestra que ciertos tipos de información como datos “capturados” por expertos son relativamente precisos y exactos, mientras que aquellos “generados” empíricamente no lo fueron. Se concluye con algunas ideas sobre cómo los miembros de la Sociedad Americana de Pesquerías pueden mejorar los datos disponibles en FishBase.
An evaluation of alternative assessment approaches for intermixing fish populations: a case study with Great Lakes lake whitefish
Authors: Li Yang , Bence James R. , Brenden Travis O. 
Published: April 2014

AbstractWe used simulation modeling to explore how three statistical catch-at-age approaches for assessing intermixed fisheries performed in terms of assessment accuracy and management performance, under differing productivity, mixing, and harvest levels. Simulations were based on intermixing lake whitefish (Coregonus clupeaformis) populations in the upper Laurentian Great Lakes of North America. We found that with intermixing, the “separate” assessment approach, which ignored intermixing and treated mixed populations as unit stocks, produced biased estimates of spawning stock biomass (SSB); however, the “pooled” assessment approach, which lumped populations and assessed them as a single stock, was nearly unbiased in estimating SSB. The “overlap” assessment approach, which estimated the populations in one combined assessment model by incorporating actual mixing rates, was most strongly biased in estimating SSB in the absence of mixing, with bias decreasing as mixing levels increased. With high mixing levels, the overlap method had difficulty converging on unique solutions. The pooled approach provided better management performance than the separate approach with intermixing. When the overlap method could be applied, it provided the greatest SSB with little reductions in yield and the lowest inter-annual variation in yield. Relative performances of the assessment approaches were robust to assumed harvest levels.
Comparative Studies on Composition and Distribution of Phenolic Acids in Cereal Grain Botanical Fractions
Authors: Ndolo Victoria U. , Beta Trust 
Published: April 2014

ABSTRACTThe phenolic acid composition and concentration of four manually separated fractions (pericarp, aleurone layer, germ, and endosperm fractions) as well as whole grains of yellow corn, wheat, barley, and oats were analyzed by HPLC‐MS/MS following microwave‐assisted alkaline aqueous extraction. Phenolic acid compositions in whole grains and their fractions were similar, with minor differences among the grain fractions. Significant differences (P < 0.05), however, were observed in phenolic acid concentrations among cereal types, within cereal varieties, and among grain fractions, with yellow corn exhibiting the highest values. The concentrations of p‐coumaric and syringic acid in the pericarp were 10‐ to 15‐fold and 6‐ to 10‐fold higher, respectively, in yellow corn than in wheat, barley, and oats. In the aleurone layer, sinapic and vanillic acids in yellow corn were about 8‐ and 30‐fold more than in wheat. The germ fraction of wheat had 1.8 times more syringic acid than yellow corn germ. Grain fractions, excluding endosperm, had enhanced levels of phenolic acids compared with whole grain. Sinapic acid was more concentrated in the pericarp and germ of wheat, whereas isoferulic acid was concentrated in the germ of purple barley. Syringic and vanillic acids were concentrated in the pericarp and sinapic acid in the aleurone layer of yellow corn. These findings are important in understanding the composition and distribution of phenolic acids, and they act as a guide in identification of grain fractions for use as food ingredients. In addition, yellow corn fractions (aleurone and pericarp) may be potential alternative phenolic‐rich functional food ingredients in grain‐based food products.
Integrated Analysis Platform: An Open-Source Information System for High-Throughput Plant Phenotyping
Authors: Klukas Christian , Chen Dijun , Pape Jean-Michel 
Published: April 2014

Abstract
High-throughput phenotyping is emerging as an important technology to dissect phenotypic components in plants. Efficient image processing and feature extraction are prerequisites to quantify plant growth and performance based on phenotypic traits. Issues include data management, image analysis, and result visualization of large-scale phenotypic data sets. Here, we present Integrated Analysis Platform (IAP), an open-source framework for high-throughput plant phenotyping. IAP provides user-friendly interfaces, and its core functions are highly adaptable. Our system supports image data transfer from different acquisition environments and large-scale image analysis for different plant species based on real-time imaging data obtained from different spectra. Due to the huge amount of data to manage, we utilized a common data structure for efficient storage and organization of data for both input data and result data. We implemented a block-based method for automated image processing to extract a representative list of plant phenotypic traits. We also provide tools for build-in data plotting and result export. For validation of IAP, we performed an example experiment that contains 33 maize (Zea mays ‘Fernandez’) plants, which were grown for 9 weeks in an automated greenhouse with nondestructive imaging. Subsequently, the image data were subjected to automated analysis with the maize pipeline implemented in our system. We found that the computed digital volume and number of leaves correlate with our manually measured data in high accuracy up to 0.98 and 0.95, respectively. In summary, IAP provides a multiple set of functionalities for import/export, management, and automated analysis of high-throughput plant phenotyping data, and its analysis results are highly reliable.
The Middle Class ‘at Home among the Poor’ — How Social Mix is Lived in Parisian Suburbs: Between Local Attachment and Metropolitan Practices
Authors: Bacqué Marie‐Hélène , Charmes Eric , Vermeersch Stéphanie 
Published: April 2014

AbstractHow do households belonging to the middle classes decide to come live in a ‘poor’ city in the Parisian suburbs? What makes them stay? What are the judgements and strategies that have been brought to bear both individually in their daily lives and as a social group in terms of their collective involvement and their relationships with other social groups? What does this kind of ‘social mix’ imply in terms of social practices, local and social belonging? This article shows that attitudes towards social mixing have to be considered in terms of their sociological dimensions. This analysis thus takes into account middle‐class diversity in socio‐residential terms, in terms of trajectories, values and attachment to a particular area. The article also emphasizes the importance of distinguishing between different dimensions of attitudes towards social mixing: depending on the issues at stake, people can accept and sometimes promote a form of cohabitation, or, quite to the contrary, reject it. Finally, the article emphasizes the importance of local contexts and their temporality: for someone belonging to the middle classes, living in a poor city may also mean holding a relatively higher position than elsewhere.
Disparities in pre‐eclampsia and eclampsia among immigrant women giving birth in six industrialised countries
Authors: Urquia ML , Glazier RH , Gagnon AJ , Mortensen LH , Nybo Andersen A‐M , Janevic T , Guendelman S , Thornton D , Bolumar F , Río Sánchez I , Small R , Davey M‐A , Hjern A ,   the ROAM Collaboration
Published: April 2014

ObjectiveTo assess disparities in pre‐eclampsia and eclampsia among immigrant women from various world regions giving birth in six industrialised countries.DesignCross‐country comparative study of linked population‐based databases.SettingProvincial or regional obstetric delivery data from Australia, Canada, Spain and the USA and national data from Denmark and Sweden.PopulationAll immigrant and non‐immigrant women delivering in the six industrialised countries within the most recent 10‐year period available to each participating centre (1995–2010).MethodsData was collected using standardised definitions of the outcomes and maternal regions of birth. Pooled data were analysed with multilevel models. Within‐country analyses used stratified logistic regression to obtain odds ratios (OR) with 95% confidence intervals (95% CI).Main outcome measuresPre‐eclampsia, eclampsia and pre‐eclampsia with prolonged hospitalisation (cases per 1000 deliveries).ResultsThere were 9 028 802 deliveries (3 031 399 to immigrant women). Compared with immigrants from Western Europe, immigrants from Sub‐Saharan Africa and Latin America & the Caribbean were at higher risk of pre‐eclampsia (OR: 1.72; 95% CI: 1.63, 1.80 and 1.63; 95% CI: 1.57, 1.69) and eclampsia (OR: 2.12; 95% CI: 1.61, 2.79 and 1.55; 95% CI: 1.26, 1. 91), respectively, after adjustment for parity, maternal age and destination country. Compared with native‐born women, European and East Asian immigrants were at lower risk in most industrialised countries. Spain exhibited the largest disparities and Australia the smallest.ConclusionImmigrant women from Sub‐Saharan Africa and Latin America & the Caribbean require increased surveillance due to a consistently high risk of pre‐eclampsia and eclampsia.
Radiation Resistance and Loss of Crystal Violet Binding Activity in Yersinia enterocolitica Suspended in Raw Ground Pork Exposed to Gamma Radiation and Modified Atmosphere
Authors: Bhaduri Saumya , Sheen Shiowshuh , Sommers Christopher H. 
Published: April 2014

AbstractVirulence of many foodborne pathogens is directly linked to genes carried on self‐replicating extra‐chromosomal elements, which can transfer genetic material, both vertically and horizontally, between bacteria of the same and different species. Pathogenic Yersinia enterocolitica harbors a 70‐kb virulence plasmid (pYV) that encodes genes for low calcium response, crystal violet (CV) binding, Congo red uptake, autoagglutination (AA), hydrophobicity (HP), type III secretion channels, host immune suppression factors, and biofilm formation. Ionizing radiation and modified atmosphere packaging (MAP) are used to control foodborne pathogens and meat spoilage. In this study, the effect of gamma radiation and modified atmosphere (air, 100% N2, 75% N2: 25% CO2, 50% N2: 50% CO2, 25% N2: 75% CO2, 100% CO2) were examined by using the CV binding phenotype, for the presence or absence of pYV in Y. enterocolitica, suspended in raw ground pork. All Y. enterocolitica serovars used (O:3, O:8, and O5,27) were more sensitive to radiation as the CO2 concentration increased above 50%. Crystal violet binding following a radiation dose of 1.0 kGy, which reduced the Y. enterocolitica serovars >5 log, was greatest in the presence of air (ca. 8%), but was not affected by N2 or CO2 concentration (ca. 5%). Following release from modified atmosphere after irradiation, the loss of CV binding rose from 5% to 8% immediately following irradiation to >30% after outgrowth at 25 °C for 24 h. These results, using Y. enterocolitica as a model system, indicate that the risk of foodborne illness could be affected by the loss of virulence factors when postprocess intervention technologies are used.Practical ApplicationProvides gamma radiation D10 data for inactivation data for Y. enterocolitica irradiated under modified atmosphere and information to risk assessors regarding the difference between pathogen presence versus actual virulence.
Impact of Formulation and Saliva on Acid Milk Gel Friction Behavior
Authors: Joyner (Melito) Helen S. , Pernell Chris W. , Daubert Christopher R. 
Published: April 2014

AbstractRheological analysis is commonly used to evaluate mechanical properties in studies of food behavior. However, rheological analysis is often insufficient to describe food texture as evaluated by descriptive sensory analysis. Additionally, traditional rheometry does not account for changes in food behavior as a function of saliva incorporation into the food during mastication. The objectives of this study were to evaluate friction behavior of acid milk gels with and without the addition of saliva, and to determine relationships between frictional behaviors and mechanical and sensory behaviors. Acid milk gels were prepared with 12.5% total solids comprising nonfat dry milk, whey protein isolate, waxy maize starch, and gelatin in different ratios. The addition of starch was found to have significant impact on acid milk gel frictional behavior. Addition of saliva resulted in a change in frictional behavior over the entire sliding speed range measured. Correlations were found between rheological, tribological, and sensory behavior, suggesting that an underlying mechanism may impact both viscosity and friction behavior. Additional study is needed to further explore the links between food structure, rheology, tribology, and sensory texture.Practical ApplicationApplication of tribology in food science allows measurement of friction behavior of foods. Matching both rheological and tribological behavior is important to creating reduced‐fat or reduced‐sugar products with similar mouthfeel to the original product.
Assessment of Microbiological Contamination of Fresh, Minimally Processed, and Ready‐to‐Eat Lettuces (Lactuca sativa), Rio de Janeiro State, Brazil
Authors: Brandão Marcelo L. L. , Almeida Davi O. , Bispo Fernanda C. P. , Bricio Silvia M. L. , Marin Victor A. , Miagostovich Marize P. 
Published: April 2014

AbstractThis study aimed to assess the microbiological contamination of lettuces commercialized in Rio de Janeiro, Brazil, in order to investigate detection of norovirus genogroup II (NoV GII), Salmonella spp., total and fecal coliforms, such as Escherichia coli. For NoV detection samples were processed using the adsorption‐elution concentration method associated to real‐time quantitative polymerase chain reaction (qPCR). A total of 90 samples of lettuce including 30 whole fresh lettuces, 30 minimally processed (MP) lettuces, and 30 raw ready‐to‐eat (RTE) lettuce salads were randomly collected from different supermarkets (fresh and MP lettuce samples), food services, and self‐service restaurants (RTE lettuce salads), all located in Rio de Janeiro, Brazil, from October 2010 to December 2011. NoV GII was not detected and PP7 bacteriophage used as internal control process (ICP) was recovered in 40.0%, 86.7%, and 76.7% of those samples, respectively. Salmonella spp. was not detected although fecal contamination has been observed by fecal coliform concentrations higher than 102 most probable number/g. E. coli was detected in 70.0%, 6.7%, and 30.0% of fresh, MP, and RTE samples, respectively. This study highlights the need to improve hygiene procedures at all stages of vegetable production and to show PP7 bacteriophage as an ICP for recovering RNA viruses’ methods from MP and RTE lettuce samples, encouraging the evaluation of new protocols that facilitate the establishment of methodologies for NoV detection in a greater number of food microbiology laboratories.Practical ApplicationThe PP7 bacteriophage can be used as an internal control process in methods for recovering RNA viruses from minimally processed and ready‐to‐eat lettuce samples.