bluuebunny/crossref_metadata_2025_split huggingface dataset:
Iodine status during pregnancy in India and related neonatal and infant outcomes
Authors: Lean Morven IFA , Lean Mike EJ , Yajnik Chittaranjan S , Bhat Dattatray S , Joshi Suyog M , Raut Deepa A , Lubree Himangi G , Combet Emilie 
Published: May 2013

AbstractObjectiveTo document iodine status in Indian pregnancies, associations with maternal diet and demographics, and offspring developmental measures.DesignLongitudinal study following mothers through pregnancy and offspring up to 24 months.SettingRural health-care centre (Vadu) and urban antenatal clinic (Pune) in the Maharashtra region of India.SubjectsPregnant mothers at 17 (n132) and 34 weeks’ (n151) gestation and their infants from birth to the age of 24 months.ResultsMedian urinary iodine concentration (UIC) was 203 and 211 μg/l at 17 and 34 weeks of pregnancy, respectively (range 26–800 μg/l). Using the UIC distribution adjusted for within-person variation, extreme UIC quartiles were compared for predictors and outcomes. There was no correlation between UIC at 17 and 34 weeks, but 24 % of those with UIC in the lowest quartile at 17 weeks had UIC in the same lowest quartile at 34 weeks. Maternal educational, socio-economic status and milk products consumption (frequency) were different between the lowest and highest quartile of UIC at 34 weeks. Selected offspring developmental outcomes differed between the lowest and highest UIC quartiles (abdominal circumference at 24 months, subscapular and triceps skinfolds at 12 and 24 months). However, UIC was only a weak predictor of subscapular skinfold at 12 months and of triceps skinfold at 24 months.ConclusionsMedian UIC in this pregnant population suggested adequate dietary provision at both gestational stages studied. Occasional high results found in spot samples may indicate intermittent consumption of iodine-rich foods. Maternal UIC had limited influence on offspring developmental outcomes.
Dietary patterns and the risk of non-Hodgkin lymphoma
Authors: Ollberding Nicholas J , Aschebrook-Kilfoy Briseis , Caces Donne Bennett D , Smith Sonali M , Weisenburger Dennis D , Chiu Brian C-H 
Published: May 2013

AbstractObjectivePrevious studies examining the role of single foods or nutrients in the aetiology of non-Hodgkin lymphoma (NHL) have produced inconsistent findings. Few studies have examined associations for dietary patterns, which may more accurately reflect patterns of consumption and the complexity of dietary intake. The objective of the present study was to examine whether dietary patterns identified by factor analysis were associated with NHL risk.DesignCase–control.SettingPopulation-based sample residing in Nebraska from 1999 to 2002.SubjectsA total of 336 cases and 460 controls.ResultsFactor analysis identified two major dietary patterns: (i) a ‘Meat, Fat and Sweets’ dietary pattern characterized by high intakes of French fries, red meat, processed meat, pizza, salty snacks, sweets and desserts, and sweetened beverages; and (ii) a ‘Fruit, Vegetables and Starch’ dietary pattern characterized by high intakes of vegetables, fruit, fish, and cereals and starches. In multivariable logistic regression models, the ‘Meat, Fat and Sweets’ dietary pattern was associated with an increased risk of overall NHL (ORQ4v.Q1 = 3·6, 95 % CI 1·9, 6·8; Ptrend = 0·0004), follicular lymphoma (ORQ4v.Q1 = 3·1, 95 % CI 1·2, 8·0; Ptrend = 0·01), diffuse large B-cell lymphoma (ORQ4v.Q1 = 3·2, 95 % CI 1·1, 9·0; Ptrend = 0·09) and marginal zone lymphoma (ORQ4v.Q1 = 8·2, 95 % CI 1·3, 51·2; Ptrend = 0·05). No association with overall or subtype-specific risk was detected for the ‘Fruit, Vegetables and Starch’ dietary pattern. No evidence of heterogeneity was detected across strata of age, sex, BMI, smoking status or alcohol consumption.ConclusionsOur results suggest that a dietary pattern high in meats, fats and sweets may be associated with an increased risk of NHL.
Remineralization of Demineralized Enamel by Toothpastes: A Scanning Electron Microscopy, Energy Dispersive X-Ray Analysis, and Three-Dimensional Stereo-Micrographic Study
Authors: Gjorgievska Elizabeta S. , Nicholson John W. , Slipper Ian J. , Stevanovic Marija M. 
Published: May 2013

AbstractRemineralization of hard dental tissues is thought to be a tool that could close the gap between prevention and surgical procedures in clinical dentistry. The purpose of this study was to examine the remineralizing potential of different toothpaste formulations: toothpastes containing bioactive glass, hydroxyapatite, or strontium acetate with fluoride, when applied to demineralized enamel. Results obtained by scanning electron microscopy (SEM) and SEM/energy dispersive X-ray analyses proved that the hydroxyapatite and bioactive glass-containing toothpastes were highly efficient in promoting enamel remineralization by formation of deposits and a protective layer on the surface of the demineralized enamel, whereas the toothpaste containing 8% strontium acetate and 1040 ppm fluoride as NaF had little, if any, remineralization potential. In conclusion, the treatment of demineralized teeth with toothpastes containing hydroxyapatite or bioactive glass resulted in repair of the damaged tissue.
Examination of Biologically Active Nanocomplexes by Nanoparticle Tracking Analysis
Authors: Nikitin Nikolai , Trifonova Ekaterina , Karpova Olga , Atabekov Joseph 
Published: May 2013

AbstractNanoparticle tracking analysis (NTA) was first applied to biologically active nanocomplexes to obtain concurrent information on their size, state of aggregation, concentration, and antigenic specificity in liquid. The subject of the NTA was an immunogenic complex (a candidate nanovaccine) comprised of spherical particles (SPs) generated by thermal remodeling of the tobacco mosaic virus and Rubella virus tetraepitopes exposed on the surface of SP.
Chromatic Aberration-Corrected Tilt Series Transmission Electron Microscopy of Nanoparticles in a Whole Mount Macrophage Cell
Authors: Baudoin Jean-Pierre , Jinschek Joerg R. , Boothroyd Chris B. , Dunin-Borkowski Rafal E. , de Jonge Niels 
Published: May 2013

AbstractTransmission electron microscopy (TEM) in combination with electron tomography is widely used to obtain nanometer scale three-dimensional (3D) structural information about biological samples. However, studies of whole eukaryotic cells are limited in resolution and/or contrast on account of the effect of chromatic aberration of the TEM objective lens on electrons that have been scattered inelastically in the specimen. As a result, 3D information is usually obtained from sections and not from whole cells. Here, we use chromatic aberration-corrected TEM to record bright-field TEM images of nanoparticles in a whole mount macrophage cell. Tilt series of images are used to generate electron tomograms, which are analyzed to assess the spatial resolution that can be achieved for different vertical positions in the specimen. The uptake of gold nanoparticles coated with low-density lipoprotein (LDL) is studied. The LDL is found to assemble in clusters. The clusters contain nanoparticles taken up on different days, which are joined without mixing their nanoparticle cargo.
A prospective study of patients with impending spinal cord compression treated with palliative radiotherapy alone
Authors: O'Sullivan L. , Clayton-Lea A. , McArdle O. , McGarry M. , Kenny J. , Dunne M. , O'Shea E. , Small C. , Moriarty M. , Thirion P. 
Published: May 2013

AbstractImpending malignant spinal cord compression (IMSCC) may be defined as compression of the thecal sac, without any visible pressure on the spinal cord itself. Although there is a perception that IMSCC patients have a better prognosis and less severe clinical symptoms than true malignant spinal cord compression (MSCC) patients, these factors have never been documented in the literature.PurposeTo record the characteristics, management and functional outcome of a group of patients with IMSCC, who were treated with radiotherapy in our institution, and compare these parameters with similar data on MSCC patients.Materials and methodsData (gender, age, primary oncological diagnosis, pain, performance status and neurological status) were prospectively collected for 28 patients. Patients were then followed up post treatment to document their response to treatment and treatment-related toxicity.ResultsThe median survival of our group of IMSCC patients is similar to that of an MSCC patient. In addition, the IMSCC group exhibits significant clinical symptoms including neurological deficit.ConclusionAlthough further studies are necessary, we have found that IMSCC patients in this study share similar prognosis and clinical symptoms with MSCC patients. Clinicians should be aware of this when communicating with IMSCC patients and their families, and short-course radiotherapy should be considered.
Chytrid epidemics may increase genetic diversity of a diatom spring-bloom
Authors: Gsell Alena S , de Senerpont Domis Lisette N , Verhoeven Koen J F , van Donk Ellen , Ibelings Bastiaan W 
Published: May 2013

Abstract
Contrary to expectation, populations of clonal organisms are often genetically highly diverse. In phytoplankton, this diversity is maintained throughout periods of high population growth (that is, blooms), even though competitive exclusion among genotypes should hypothetically lead to the dominance of a few superior genotypes. Genotype-specific parasitism may be one mechanism that helps maintain such high-genotypic diversity of clonal organisms. Here, we present a comparison of population genetic similarity by estimating the beta-dispersion among genotypes of early and peak bloom populations of the diatom Asterionella formosa for three spring-blooms under high or low parasite pressure. The Asterionella population showed greater beta-dispersion at peak bloom than early bloom in the 2 years with high parasite pressure, whereas the within group dispersion did not change under low parasite pressure. Our findings support that high prevalence parasitism can promote genetic diversification of natural populations of clonal hosts.
Ammonia oxidation kinetics and temperature sensitivity of a natural marine community dominated by Archaea
Authors: Horak Rachel E A , Qin Wei , Schauer Andy J , Armbrust E Virginia , Ingalls Anitra E , Moffett James W , Stahl David A , Devol Allan H 
Published: May 2013

Abstract
Archaeal ammonia oxidizers (AOAs) are increasingly recognized as prominent members of natural microbial assemblages. Evidence that links the presence of AOA with in situ ammonia oxidation activity is limited, and the abiotic factors that regulate the distribution of AOA natural assemblages are not well defined. We used quantitative PCR to enumerate amoA (encodes α-subunit of ammonia monooxygenase) abundances; AOA amoA gene copies greatly outnumbered ammonia-oxidizing bacteria and amoA transcripts were derived primarily from AOA throughout the water column of Hood Canal, Puget Sound, WA, USA. We generated a Michaelis–Menten kinetics curve for ammonia oxidation by the natural community and found that the measured Km of 98±14 nmol l−1 was close to that for cultivated AOA representative Nitrosopumilus maritimus SCM1. Temperature did not have a significant effect on ammonia oxidation rates for incubation temperatures ranging from 8 to 20 °C, which is within the temperature range for depths of measurable ammonia oxidation at the site. This study provides substantial evidence, through both amoA gene copies and transcript abundances and the kinetics response, that AOA are the dominant active ammonia oxidizers in this marine environment. We propose that future ammonia oxidation experiments use a Km for the natural community to better constrain ammonia oxidation rates determined with the commonly used 15NH4+ dilution technique.
Migrating Oligodendrocyte Progenitor Cells Swell Prior to Soma Dislocation
Authors: Happel Patrick , Möller Kerstin , Schwering Nina K. , Dietzel Irmgard D. 
Published: May 2013

AbstractThe migration of oligodendrocyte progenitor cells (OPCs) to the white matter is an indispensable requirement for an intact brain function. The mechanism of cell migration in general is not yet completely understood. Nevertheless, evidence is accumulating that besides the coordinated rearrangement of the cytoskeleton, a finetuned interplay of ion and water fluxes across the cell membrane is essential for cell migration. One part of a general hypothesis is that a local volume increase towards the direction of movement triggers a mechano-activated calcium influx that regulates various procedures at the rear end of a migrating cell. Here, we investigated cell volume changes of migrating OPCs using scanning ion conductance microscopy. We found that during accelerated migration OPCs undergo an increase in the frontal cell body volume. These findings are supplemented with time lapse calcium imaging data that hint an increase in calcium content the frontal part of the cell soma.
ON THE DIRECT IMAGING OF TIDALLY HEATED EXOMOONS
Authors: Limbach Mary Anne , Turner Edwin L. 
Published: May 2013

ABSTRACT
We demonstrate the ability of existing and planned telescopes, on the ground and in space, to directly image tidally heated exomoons orbiting gas-giant exoplanets. Tidally heated exomoons can plausibly be far more luminous than their host exoplanet and as much as 0.1% as bright as the system's stellar primary if it is a low mass star. Because emission from exomoons can be powered by tidal forces, they can shine brightly at arbitrarily large separations from the system's stellar primary with temperatures of several hundreds degrees Kelvin or even higher in extreme cases. Furthermore, these high temperatures can occur in systems that are billions of years old. Tidally heated exomoons may thus be far easier targets for direct imaging studies than giant exoplanets which must be both young and at a large projected separation (typically at least tens of AU) from their primary to be accessible to current generation direct imaging studies. For example, the (warm) Spitzer Space Telescope and the next generation of ground based instruments could detect an exomoon roughly the size of the Earth at a temperature ≈600 K and a distance ≈5 pc in the K, L, and M bands at the 5σ confidence level with a one hour exposure; in more favorable but still plausible cases, detection at distances of tens of parsecs is feasible. Future mid-infrared space telescopes, such as James Webb Space Telescope and SPICA, will be capable of directly imaging tidally heated exomoons around the nearest two dozen stars with a brightness temperature ⩾300 K and R ⩾ 1 R
⊕ orbiting at ⩾12 AU from the primary star at a 5σ confidence level in a 104 s integration. In addition it is possible that some of the exoplanets which have already been directly imaged are actually tidally heated exomoons or blends of such objects with hot young planets. If such exomoons exist and are sufficiently common (i.e., nearby), it may well be far easier to directly image an exomoon with surface conditions that allow the existence of liquid water than it will be to resolve an Earth-like planet in the classical habitable zone of its primary.
PconsC: combination of direct information methods and alignments improves contact prediction
Authors: Skwark Marcin J. , Abdel-Rehim Abbi , Elofsson Arne 
Published: May 2013

Abstract
Summary: Recently, several new contact prediction methods have been published. They use (i) large sets of multiple aligned sequences and (ii) assume that correlations between columns in these alignments can be the results of indirect interaction. These methods are clearly superior to earlier methods when it comes to predicting contacts in proteins. Here, we demonstrate that combining predictions from two prediction methods, PSICOV and plmDCA, and two alignment methods, HHblits and jackhmmer at four different e-value cut-offs, provides a relative improvement of 20% in comparison with the best single method, exceeding 70% correct predictions for one contact prediction per residue.
Availability: The source code for PconsC along with supplementary data is freely available at http://c.pcons.net/
Contact: arne@bioinfo.se
Supplementary information: Supplementary data are available at Bioinformatics online.
DAPPLE: a pipeline for the homology-based prediction of phosphorylation sites
Authors: Trost Brett , Arsenault Ryan , Griebel Philip , Napper Scott , Kusalik Anthony 
Published: May 2013

Abstract
Summary: While many experimentally characterized phosphorylation sites exist for certain organisms, such as human, rat and mouse, few sites are known for other organisms, hampering related research efforts. We have developed a software pipeline called DAPPLE that automates the process of using known phosphorylation sites from other organisms to identify putative sites in an organism of interest.
Availability: DAPPLE is available as a web server at http://saphire.usask.ca.
Contact: brett.trost@usask.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
IL-7 production in murine lymphatic endothelial cells and induction in the setting of peripheral lymphopenia
Authors: Miller Corey N. , Hartigan-O’Connor Dennis J. , Lee Myeong Sup , Laidlaw Grace , Cornelissen Ivo P. , Matloubian Mehrdad , Coughlin Shaun R. , McDonald Donald M. , McCune Joseph M. 
Published: May 2013

AbstractIL-7 is a required factor for T-cell homeostasis. Because of low expression levels and poor reagent availability, the cellular sources of IL-7 have proven challenging to characterize. In this study, we describe a reporter mouse in which enhanced GFP is expressed from the endogenous Il7 locus. We show that IL-7 is produced by lymphatic endothelial cells (LECs) distributed throughout the systemic lymphatic vasculature as well as by fibroblastic reticular cells, and that phosphorylation of STAT5 in lymphocytes is higher in lymphatics than in blood. Furthermore, in nodes depleted of lymphocytes, Il7 transcription is increased in stromal but not in myeloid subsets. These data support recent findings that lymphocyte homeostasis is influenced by access to secondary lymphoid organs and point to LECs as an important in vivo source of IL-7, bathing trafficking immune cells under both resting and lymphopenic conditions.
Aspartate Aminotransferase to Platelet Ratio Index Correlates With Hepatic Cirrhosis but Not With Fibrosis in Pediatric Patients With Intestinal Failure
Authors: Díaz Juan J. , Gura Kathleen M. , Roda Juliamna , Perez‐Atayde Antonio R. , Duggan Christopher , Jaksic Tom , Lo Clifford W. 
Published: May 2013

ABSTRACTBackground and Objectives:Patients with intestinal failure (IF) require parenteral nutrition (PN) support to obtain enough nutrients to sustain growth; long‐term PN use is associated with significant liver damage. The aim of this study was to analyze the use of a noninvasive test, the aspartate aminotransferase to platelet ratio index (APRI), in the diagnosis of liver disease in pediatric patients with IF.Methods:Medical records of all Boston Children's Hospital patients who received PN and underwent a liver biopsy from January 2006 until November 2010 were reviewed. Patients with IF with a clinical diagnosis were selected. APRI was calculated as (aspartate aminotransferase [U/L]/upper normal limit) × 100/platelets (109 cells/L). Presence of fibrosis and cirrhosis was estimated using the METAVIR score in liver biopsies.Results:Sixty‐two liver biopsies from 48 patients (22 girls) were studied. Mean APRI values in the different METAVIR categories (0–1, 2–3, 4) were 1.80, 1.17, and 4.24, respectively (analysis of variance P = 0.053; Bonferroni test for cirrhosis vs fibrosis P = 0.048). APRI could significantly predict cirrhosis (odds ratio 1.2; 95% confidence interval [CI] 1.001–1.43) but not fibrosis (METAVIR 2–3, odds ratio 1.00; 95% CI 0.86–1.18). Area under the receiver operating characteristic curve for cirrhosis was 0.67 (95% CI 0.45–0.89; P = 0.13).Conclusions:APRI, a noninvasive, easy‐to‐obtain bedside test, significantly predicts cirrhosis but not fibrosis in pediatric patients with IFALD. Because the clinicians need a noninvasive test to differentiate among different stages of liver fibrosis rather than differentiating cirrhosis from normal, we cannot recommend the use of this test in pediatric patients with IFALD for this purpose.
Deciphering Herbivory-Induced Gene-to-Metabolite Dynamics in Nicotiana attenuata Tissues Using a Multifactorial Approach
Authors: Gulati Jyotasana , Kim Sang-Gyu , Baldwin Ian T. , Gaquerel Emmanuel 
Published: May 2013

Abstract
In response to biotic stresses, such as herbivore attack, plants reorganize their transcriptomes and reconfigure their physiologies not only in attacked tissues but throughout the plant. These whole-organismic reconfigurations are coordinated by a poorly understood network of signal transduction cascades. To explore tissue-based interdependencies in the resistance of Nicotiana attenuata to insect attack, we conducted time-series transcriptome and metabolome profiling of herbivory-elicited source leaves and unelicited sink leaves and roots. To probe the multidimensionality of these molecular responses, we designed a novel approach of combining an extended self-organizing maps-based dimensionality reduction method with bootstrap-based nonparametric analysis of variance models to identify the onset and context of signaling and metabolic pathway activations. We illustrate the value of this analysis by revisiting dynamic changes in the expression of regulatory and structural genes of the oxylipin pathway and by studying nonlinearities in gene-metabolite associations involved in the acyclic diterpene glucoside pathway after selectively extracting modules based on their dynamic response patterns. This novel dimensionality reduction approach is broadly applicable to capture the dynamic rewiring of gene and metabolite networks in experimental design with multiple factors.
Quantification of Extracellular Carbonic Anhydrase Activity in Two Marine Diatoms and Investigation of Its Role
Authors: Hopkinson Brian M. , Meile Christof , Shen Chen 
Published: May 2013

Abstract
Many microalgae induce an extracellular carbonic anhydrase (eCA), associated with the cell surface, at low carbon dioxide (CO2) concentrations. This enzyme is thought to aid inorganic carbon uptake by generating CO2 at the cell surface, but alternative roles have been proposed. We developed a new approach to quantify eCA activity in which a reaction-diffusion model is fit to data on 18O removal from inorganic carbon. In contrast to previous methods, eCA activity is treated as a surface process, allowing the effects of eCA on cell boundary-layer chemistry to be assessed. Using this approach, we measured eCA activity in two marine diatoms (Thalassiosira pseudonana and Thalassiosira weissflogii), characterized the kinetics of this enzyme, and studied its regulation as a function of culture pH and CO2 concentration. In support of a role for eCA in CO2 supply, eCA activity specifically responded to low CO2 rather than to changes in pH or HCO3 −, and the rates of eCA activity are nearly optimal for maintaining cell surface CO2 concentrations near those in the bulk solution. Although the CO2 gradients abolished by eCA are small (less than 0.5 μm concentration difference between bulk and cell surface), CO2 uptake in these diatoms is a passive process driven by small concentration gradients. Analysis of the effects of short-term and long-term eCA inhibition on photosynthesis and growth indicates that eCA provides a small energetic benefit by reducing the surface-to-bulk CO2 gradient. Alternative roles for eCA in CO2 recovery as HCO3 − and surface pH regulation were investigated, but eCA was found to have minimal effects on these processes.