bluuebunny/crossref_metadata_2025_split huggingface dataset:
U.S. Climate Reference Network Soil Moisture and Temperature Observations
Authors: Bell Jesse E. , Palecki Michael A. , Baker C. Bruce , Collins William G. , Lawrimore Jay H. , Leeper Ronald D. , Hall Mark E. , Kochendorfer John , Meyers Tilden P. , Wilson Tim , Diamond Howard J. 
Published: January 2013

AbstractThe U.S. Climate Reference Network (USCRN) is a network of climate-monitoring stations maintained and operated by the National Oceanic and Atmospheric Administration (NOAA) to provide climate-science-quality measurements of air temperature and precipitation. The stations in the network were designed to be extensible to other missions, and the National Integrated Drought Information System program determined that the USCRN could be augmented to provide observations that are more drought relevant. To increase the network’s capability of monitoring soil processes and drought, soil observations were added to USCRN instrumentation. In 2011, the USCRN team completed at each USCRN station in the conterminous United States the installation of triplicate-configuration soil moisture and soil temperature probes at five standards depths (5, 10, 20, 50, and 100 cm) as prescribed by the World Meteorological Organization; in addition, the project included the installation of a relative humidity sensor at each of the stations. Work is also under way to eventually install soil sensors at the expanding USCRN stations in Alaska. USCRN data are stewarded by the NOAA National Climatic Data Center, and instrument engineering and performance studies, installation, and maintenance are performed by the NOAA Atmospheric Turbulence and Diffusion Division. This article provides a technical description of the USCRN soil observations in the context of U.S. soil-climate–measurement efforts and discusses the advantage of the triple-redundancy approach applied by the USCRN.
Quantitative fluorescence loss in photobleaching for analysis of protein transport and aggregation
Authors: Wüstner Daniel , Solanko Lukasz M , Lund Frederik W , Sage Daniel , Schroll Hans J , Lomholt Michael A 
Published: January 2013

Abstract

Background
Fluorescence loss in photobleaching (FLIP) is a widely used imaging technique, which provides information about protein dynamics in various cellular regions. In FLIP, a small cellular region is repeatedly illuminated by an intense laser pulse, while images are taken with reduced laser power with a time lag between the bleaches. Despite its popularity, tools are lacking for quantitative analysis of FLIP experiments. Typically, the user defines regions of interest (ROIs) for further analysis which is subjective and does not allow for comparing different cells and experimental settings.

Results
We present two complementary methods to detect and quantify protein transport and aggregation in living cells from FLIP image series. In the first approach, a stretched exponential (StrExp) function is fitted to fluorescence loss (FL) inside and outside the bleached region. We show by reaction–diffusion simulations, that the StrExp function can describe both, binding/barrier–limited and diffusion-limited FL kinetics. By pixel-wise regression of that function to FL kinetics of enhanced green fluorescent protein (eGFP), we determined in a user-unbiased manner from which cellular regions eGFP can be replenished in the bleached area. Spatial variation in the parameters calculated from the StrExp function allow for detecting diffusion barriers for eGFP in the nucleus and cytoplasm of living cells. Polyglutamine (polyQ) disease proteins like mutant huntingtin (mtHtt) can form large aggregates called inclusion bodies (IB’s). The second method combines single particle tracking with multi-compartment modelling of FL kinetics in moving IB’s to determine exchange rates of eGFP-tagged mtHtt protein (eGFP-mtHtt) between aggregates and the cytoplasm. This method is self-calibrating since it relates the FL inside and outside the bleached regions. It makes it therefore possible to compare release kinetics of eGFP-mtHtt between different cells and experiments.

Conclusions
We present two complementary methods for quantitative analysis of FLIP experiments in living cells. They provide spatial maps of exchange dynamics and absolute binding parameters of fluorescent molecules to moving intracellular entities, respectively. Our methods should be of great value for quantitative studies of intracellular transport.
A microsatellite-based linkage map of salt tolerant tilapia (Oreochromis mossambicus x Oreochromis spp.) and mapping of sex-determining loci
Authors: Liu Feng , Sun Fei , Li Jian , Xia Jun Hong , Lin Grace , Tu Rong Jian , Yue Gen Hua 
Published: January 2013

Abstract

Background
Tilapia is the common name for a group of cichlid fishes and is one of the most important aquacultured freshwater food fish. Mozambique tilapia and its hybrids, including red tilapia are main representatives of salt tolerant tilapias. A linkage map is an essential framework for mapping QTL for important traits, positional cloning of genes and understanding of genome evolution.

Results
We constructed a consensus linkage map of Mozambique tilapia and red tilapia using 95 individuals from two F1 families and 401 microsatellites including 282 EST-derived markers. In addition, we conducted comparative mapping and searched for sex-determining loci on the whole genome. These 401 microsatellites were assigned to 22 linkage groups. The map spanned 1067.6 cM with an average inter-marker distance of 3.3 cM. Comparative mapping between tilapia and stickleback, medaka, pufferfish and zebrafish revealed clear homologous relationships between chromosomes from different species. We found evidence for the fusion of two sets of two independent chromosomes forming two new chromosome pairs, leading to a reduction of 24 chromosome pairs in their ancestor to 22 pairs in tilapias. The XY sex determination locus in Mozambique tilapia was mapped on LG1, and verified in five families containing 549 individuals. The major XY sex determination locus in red tilapia was located on LG22, and verified in two families containing 275 individuals.

Conclusions
A first-generation linkage map of salt tolerant tilapia was constructed using 401 microsatellites. Two separate fusions of two sets of two independent chromosomes may lead to a reduction of 24 chromosome pairs in their ancestor to 22 pairs in tilapias. The XY sex-determining loci from Mozambique tilapia and red tilapia were mapped on LG1 and LG22, respectively. This map provides a useful resource for QTL mapping for important traits and comparative genome studies. The DNA markers linked to the sex-determining loci could be used in the selection of YY males for breeding all-male populations of salt tolerant tilapia, as well as in studies on mechanisms of sex determination in fish.
A water extract of Samchulkunbi-tang attenuates airway inflammation by inhibiting inos and MMP-9 activities in an ovalbumin-induced murine asthma model
Authors: Lee Mee Young , Shin In Sik , Lim Hye Sun , Shin Hyeun Kyoo 
Published: January 2013

Abstract

Background
In this study, we investigated the effect of Samchulkunbi-tang water extract (SCTE) in an established mouse model of ovalbumin (OVA)-induced allergic asthma. The effects of SCTE on the production of Th1 and Th2 cytokines, eotaxin, and total and OVA-specific immunoglobulin E, inducible nitric oxide synthase expression, and matrix metalloproteinase-9 activity were measured.

Methods
Mice were sensitized on days 0 and 14 with an intraperitoneal injection of 20 μg ovalbumin (OVA) emulsified in 2 mg aluminum hydroxide in 200 μL PBS buffer. On days 21, 22, and 23, mice received an airway exposure to OVA (1%, w/v, in PBS) for 1 h. SCTE was administered orally to mice at doses of 200 and 400 mg/kg per day from days 18 to 23.

Results
SCTE reduced the number of inflammatory cells, cytokines, and chemokines in bronchoalveolar lavage fluids and iNOS expression and MMP-9 activity in mouse lung tissue. Histological studies using hematoxylin & eosin and periodic acid-schiff staining showed that SCTE substantially inhibited OVA-induced inflammatory cell infiltration in lung tissue and goblet cell hyperplasia in the airway. SCTE also reduced IL-4 and IL-13 expression in concanavalin-A-stimulated splenocytes. These results were similar to those obtained with montelukast as a positive control.

Conclusions
Collectively, these results suggest that SCTE may be an effective oral treatment for allergic airway inflammation by virtue of its anti-inflammatory activity.
Children’s reporting of food insecurity in predominately food insecure households in Texas border colonias
Authors: Nalty Courtney C , Sharkey Joseph R , Dean Wesley R 
Published: January 2013

AbstractBackgroundFood insecurity is associated with detrimental physical, psychological, behavioral, social, and educational functioning in children and adults. Greater than one-quarter of all Hispanic households in the U.S. are food insecure. Hispanic families in the U.S. comprise 30% of households with food insecurity at the child level, the most severe form of the condition.MethodsFood security discordance was evaluated among 50 Mexican-origin children ages 6–11 and their mothers living in Texas bordercoloniasfrom March to June 2010. Mothers and children were interviewed separately usingpromotora-researcher administered Spanish versions of the Household Food Security Survey Module and the Food Security Survey Module for Youth. Cohen’s kappa statistic (κ) was used to analyze dyadic agreement of food security constructs and level of food security.ResultsEighty percent of mothers reported household food insecurity while 64% of children identified food insecurity at the child level. There was slight inter-rater agreement in food security status (κ = 0.13,p = 0.15). Poor agreement was observed on the child hunger construct (κ = −0.06,p = 0.66) with fair agreement in children not eating for a full day (κ = 0.26,p < 0.01) and relying on low-cost foods (κ = 0.23,p = 0.05).ConclusionsMother and child-reported household and child-level food insecurity among this sample of limited-resource Mexican-origincoloniasresidents far surpass national estimates. While the level of dyadic agreement was poor, discordance may be attributable to parental buffering, social desirability in responses, and/or the age of children included in the present analysis. Future research should continue to explore how food security is understood from the perspectives and experiences of children and adolescents.
Daily physical activity predicts degree of insulin resistance: a cross-sectional observational study using the 2003–2004 National Health and Nutrition Examination Survey
Authors: Nelson Rachael K , Horowitz Jeffrey F , Holleman Robert G , Swartz Ann M , Strath Scott J , Kriska Andrea M , Richardson Caroline R 
Published: January 2013

Abstract

Background
This study examined the independent association of objectively measured physical activity on insulin resistance while controlling for confounding variables including: cardiorespiratory fitness, adiposity, sex, age, and smoking status.

Methods
Data were obtained from National Health and Nutrition Examination Survey 2003–2004, a cross-sectional observational study conducted by the National Center for Health Statistics of the Centers for Disease Control that uses a stratified, multistage probability design to obtain a nationally representative sample of the U.S. population. The analysis included 402 healthy U.S. adults with valid accelerometer, cardiorespiratory fitness, and fasting plasma glucose and insulin concentrations. After controlling for relevant confounding variables we performed a multiple linear regression to predict homeostatic model of insulin resistance (HOMA-IR) based on average daily minutes of moderate-to-vigorous physical activity (MVPA).

Results
In our bivariate models, MVPA, cardiorespiratory fitness and body fat percentage were all significantly correlated with log HOMA-IR. In the complete model including MVPA and relevant confounding variables, there were strong and significant associations between MVPA and log HOMA-IR (β= −0.1607, P=0.004). In contrast the association between cardiorespiratory fitness and log HOMA-IR was not significant.

Conclusion
When using an objective measure of physical activity the amount of time engaged in daily physical activity was associated with lower insulin resistance, whereas higher cardiorespiratory fitness was not. These results suggest that the amount of time engaged in physical activity may be an important determinant for improving glucose metabolism.
Towards an effective control programme of soil-transmitted helminth infections among Orang Asli in rural Malaysia. Part 1: Prevalence and associated key factors
Authors: Nasr Nabil A , Al-Mekhlafi Hesham M , Ahmed Abdulhamid , Roslan Muhammad Aidil , Bulgiba Awang 
Published: January 2013

Abstract

Background
Despite the continuous efforts to improve the quality of life of Orang Asli (Aborigines) communities, these communities are still plagued with a wide range of health problems including parasitic infections. The first part of this study aimed at determining the prevalence of soil-transmitted helminth (STH) infections and identifying their associated factors among rural Orang Asli children.

Methods
A cross-sectional study was carried out among 484 Orang Asli children aged ≤ 15 years (235 females and 249 males) belonging to 215 households from 13 villages in Lipis district, Pahang, Malaysia. Faecal samples were collected and examined by using formalin-ether sedimentation, Kato Katz and Harada Mori techniques. Demographic, socioeconomic, environmental and behavioural information were collected by using a pre-tested questionnaire.

Results
Overall, 78.1% of the children were found to be infected with one or more STH species. The prevalence of trichuriasis, ascariasis and hookworm infections were 71.7%, 37.4% and 17.6%, respectively. Almost all, three quarters and one fifth of trichuriasis, ascariasis and hookworm infections, respectively, were of moderate-to-heavy intensities. Multiple logistic regression analysis showed that age of ≥ 6 years (school-age), using unsafe water supply as a source for drinking water, absence of a toilet in the house, large family size (≥ 7 members), not washing hands before eating, and not washing hands after defecation were the key factors significantly associated with STH among these children.

Conclusion
This study reveals an alarmingly high prevalence of STH among Orang Asli children and clearly brings out an urgent need to implement school-based de-worming programmes and other control measures like providing a proper sanitation, as well as a treated drinking water supply and proper health education regarding good personal hygiene practices. Such an integrated control program will help significantly in reducing the prevalence and intensity of STH in Orang Asli communities.
Droplet Digital PCR Measurement of HER2 Copy Number Alteration in Formalin-Fixed Paraffin-Embedded Breast Carcinoma Tissue
Authors: Belgrader Phillip , Tanner Stephanie C , Regan John F , Koehler Ryan , Hindson Benjamin J , Brown Alexandra S 
Published: January 2013

BACKGROUND
Human epidermal growth factor receptor 2 (HER2) testing is routinely performed by immunohistochemistry (IHC) and/or fluorescence in situ hybridization (FISH) analyses for all new cases of invasive breast carcinoma. IHC is easier to perform, but analysis can be subjective and variable. FISH offers better diagnostic accuracy and added confidence, particularly when it is used to supplement weak IHC signals, but it is more labor intensive and costly than IHC. We examined the performance of droplet digital PCR (ddPCR) as a more precise and less subjective alternative for quantifying HER2 DNA amplification.

METHODS
Thirty-nine cases of invasive breast carcinoma containing ≥30% tumor were classified as positive or negative for HER2 by IHC, FISH, or both. DNA templates for these cases were prepared from formalin-fixed paraffin-embedded (FFPE) tissues to determine the HER2 copy number by ddPCR. ddPCR involved emulsifying hydrolysis probe–based PCR reaction mixtures containing the ERBB2 [v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian); also known as HER2] gene and chromosome 17 centromere assays into nanoliter-sized droplets for thermal cycling and analysis.

RESULTS
ddPCR distinguished, through differences in the level of HER2 amplification, the 10 HER2-positive samples from the 29 HER2-negative samples with 100% concordance to HER2 status obtained by FISH and IHC analysis. ddPCR results agreed with the FISH results for the 6 cases that were equivocal by IHC analyses, confirming 2 of these samples as positive for HER2 and the other 4 as negative.

CONCLUSIONS
ddPCR can be used as a molecular-analysis tool to precisely measure copy number alterations in FFPE samples of heterogeneous breast tumor tissue.
Development and demonstration of a new SANEX Partitioning Process for selective actinide(III)/lanthanide(III) separation using a mixture of CyMe4BTBP and TODGA
Authors: Modolo Giuseppe , Wilden A. , Daniels H. , Geist Andreas , Magnusson Daniel , Malmbeck Rikard 
Published: January 2013

Abstract
Within the framework of the European collaborative project ACSEPT, a new SANEX partitioning process was developed at Forschungszentrum Jülich for the separation of the trivalent minor actinides americium, curium and californium from lanthanide fission products in spent nuclear fuels. The development is based on batch solvent extraction studies, single-centrifugal contactor tests and on flow-sheet design by computer code calculations. The used solvent is composed of 6,6´-bis(5,5,8,8-tetramethyl-5,6,7,8-tetrahydrobenzo-[1,2-4]trizazin-3-yl)-[2,2´]-bipyridine (CyMe4BTBP) and N,N,N´,N´-tetraoctyldiglycolamide (TODGA) dissolved in n-octanol. A spiked continuous counter-current test was carried out in miniature centrifugal contactors with the aid of a 20-stage flow-sheet consisting of 12 extraction, 4 scrubbing and 4 stripping stages. A product fraction containing more than 99.9% of the trivalent actinides Am(III), Cm(III) and Cf(III) was obtained. High product/feed decontamination factors >1000 were achieved for these actinides. The trivalent lanthanides were directed to the raffinate of the process with the actinide (III) product stream being contaminated with less than 0.5 mass-% in the initial lanthanides.
Effect of Water on the Densities and Viscosities of Some Ionic Liquids Containing a Phosphonium Cation
Authors: Yoo Brian , Afzal Waheed , Prausnitz John M. 
Published: January 2013

Abstract
A small amount of water can significantly decrease the viscosity of an ionic liquid. From 25–80 ºC, densities and viscosities were measured for dilute solutions of water in six ionic liquids: trihexyltetradecylphosphonium bis(2,4,4-trimethylpentyl)phosphinate, trihexyltetradecylphosphonium dicyanamide, tributyltetradecylphosphonium dodecylbenzenesulfonate, 1-ethyl,3-methylimidazolium bis(triflouromethylsulfonyl)imide, methyltrioctylammonium bis(trifluoromethylsulfonyl)imide, and triisobutylmethylphosphonium tosylate. At 25 ºC, when the water content is about 1 wt. %, the viscosity of a phosphonium-based ionic liquid is reduced by nearly one order of magnitude.
Real-Time Prediction of Complex Hydraulic Fracture Behaviour in Unconventional Naturally Fractured Reservoirs
Authors: Keshavarzi R.. , Jahanbakhshi R.. 
Published: January 2013

AbstractDetermining the propagation behavior of hydraulic fracture and the most important parameters that affect hydraulic fracturing propagation are important challenges in reservoirs with natural fractures. Hydraulic fracturing in the presence of natural fractures alters the way the induced fracture propagates through the rock and causes a complex network of fractures which can significantly influence the overall geometry and effectiveness of hydraulic fractures. Interaction of hydraulic fracture with natural fractures can lead to pre-mature screen-out, arrest of the fracture propagation, formation of multiple fractures and fracture offsets. In this study, hydraulic and natural fracture interaction in naturally fractured reservoirs has been investigated through an artificial intelligence method. So, a new feed-forward with back-propagation artificial neural network approach has been developed to predict hydraulic fracturing path due to interaction with natural fracture followed by forward selection sensitivity analysis to determine the most influential parameters. Effective parameters in hydraulic and natural fracture interaction such as horizontal differential stress, angle of approach, interfacial coefficient of friction, young’s modulus of the rock and flow rate of fracturing fluid are the inputs and hydraulic fracturing path (turning into/crossing natural fracture) when it encounters a natural fracture is the output of the developed artificial neural network. The results have shown high potentiality of the developed artificial neural network approach for real-time prediction of hydraulic fracturing path due to interaction with natural fracture. Also, the result of sensitivity analysis has shown that the angle of approach, horizontal differential stress and interfacial coefficient of friction are the macro-parameters and flow rate of fracturing fluid and young’s modulus of the rock are the micro-parameters affecting hydraulic fracture behaviour in naturally fractured reservoirs.
The Correlation of Neutron and Density Logs and its Application in Tight Gas Reservoirs Identification
Authors: Tang Wen , Liu Xiao-Peng , Hu Xiao-Xin , Zhang Xiao-Ling , Wang Shang-Xu 
Published: January 2013

Abstract
It’s a great challenge for petrophysicsts and log analysts in identifying tight gas rservoirs from conventional resistivity logs due to the complicated pore structure, thus leads to high irreducible water saturation. The resistivity contrast between tight gas bearing reservoirs and pure water saturated layers is lower than 2.0. The neutron and density logs, which are used for reservoir porosity estimation, are usable in gas bearing formation identification. In gas bearing formation, the neutron derived porosity is lower than the ture formation porosity due to the effection of excavation effect, and the density derived porosity is higher than the true formation porosity. Thus, porosity estimated from density logs is increased and the neutron derived porosity is decreased, the negative correlation exists between these two derived porosity in tight gas bearing formations. On the contrary, with the increasing of neureon porosity, the density derived porosity also increase, the positive correlation exists between them. Based on these two different correlations between tight gas bearing sands and water bearing formation, a technique, which is used to quantitatively characterize the correlation factor, is proposed and the corresponding correlation function is established. For tight gas resercoirs, the value of the correlation factor is negative, and in water saturated formations, its value is positive. Case studies from two tight gas reservoirs in China illustrate that the proposed technique is available in tight gas sands identification.