bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and evaluation of the Oxford WebQ, a low-cost, web-based method for assessment of previous 24 h dietary intakes in large-scale prospective studies
Authors: Liu Bette , Young Heather , Crowe Francesca L , Benson Victoria S , Spencer Elizabeth A , Key Timothy J , Appleby Paul N , Beral Valerie 
Published: June 2011

AbstractObjectivesTo describe the development of the Oxford WebQ, a web-based 24 h dietary assessment tool developed for repeated administration in large prospective studies; and to report the preliminary assessment of its performance for estimating nutrient intakes.DesignWe developed the Oxford WebQ by repeated testing until it was sufficiently comprehensive and easy to use. For the latest version, we compared nutrient intakes from volunteers who completed both the Oxford WebQ and an interviewer-administered 24 h dietary recall on the same day.SettingOxford, UK.SubjectsA total of 116 men and women.ResultsThe WebQ took a median of 12·5 (interquartile range: 10·8–16·3) min to self-complete and nutrient intakes were estimated automatically. By contrast, the interviewer-administered 24 h dietary recall took 30 min to complete and 30 min to code. Compared with the 24 h dietary recall, the mean Spearman's correlation for the 21 nutrients obtained from the WebQ was 0·6, with the majority between 0·5 and 0·9. The mean differences in intake were less than ±10 % for all nutrients except for carotene and vitamins B12and D. On rare occasions a food item was reported in only one assessment method, but this was not more frequent or systematically different between the methods.ConclusionsCompared with an interviewer-based 24 h dietary recall, the WebQ captures similar food items and estimates similar nutrient intakes for a single day's dietary intake. The WebQ is self-administered and nutrients are estimated automatically, providing a low-cost method for measuring dietary intake in large-scale studies.
Parent calcium-rich-food practices/perceptions are associated with calcium intake among parents and their early adolescent children
Authors: Reicks Marla , Degeneffe Dennis , Ghosh Koel , Bruhn Christine , Goodell L Suzanne , Gunther Carolyn , Auld Garry , Ballejos Miriam , Boushey Carol , Cluskey Mary , Misner Scottie , Olson Beth , Wong SiewSun , Zaghloul Sahar 
Published: June 2011

AbstractObjectiveThe study aimed to (i) segment parents of early adolescents into subgroups according to their Ca-rich-food (CRF) practices and perceptions regarding early adolescent CRF intake and (ii) determine whether Ca intake of parents and early adolescents differed by subgroup.DesignA cross-sectional convenience sample of 509 parents and their early adolescent children completed a questionnaire in 2006–2007 to assess parent CRF practices and perceptions and to estimate parent and child Ca intakes.SettingSelf-administered questionnaires were completed in community settings or homes across nine US states.SubjectsParents self-reporting as Asian, Hispanic or non-Hispanic White with a child aged 10–13 years were recruited through youth or parent events.ResultsThree parent CRF practice/perception segments were identified, including ‘Dedicated-Milk Providers/Drinkers’ (49 %), ‘Water Regulars’ (30 %) and ‘Sweet-Drink-Permissive Parents’ (23 %). Dedicated-Milk Providers/Drinkers were somewhat older and more likely to be non-Hispanic White than other groups. Ca intakes from all food sources, milk/dairy foods and milk only, and milk intakes, were higher among early adolescent children of Dedicated-Milk Providers/Drinkers compared with early adolescents of parents in other segments. Soda pop intakes were highest for early adolescents with parents in the Water Regulars group than other groups. Dedicated-Milk Providers/Drinkers scored higher on culture/tradition, health benefits and ease of use/convenience subscales and lower on a dairy/milk intolerance subscale and were more likely to report eating family dinners daily than parents in the other groups.ConclusionsParent education programmes should address CRF practices/perceptions tailored to parent group to improve Ca intake of early adolescent children.
The Influence of Receiver Size on Magnitude of Acoustic and Perceived Measures of Occlusion
Authors: Vasil-Dilaj Kristin A. , Cienkowski Kathleen M. 
Published: June 2011

Purpose
The current study examined measured and perceived occlusion for a receiver-in-the-canal (RIC) hearing aid with different-sized receivers. The relationship between these measures and ear canal volume was also investigated.

Method
Thirty adult participants were fitted with an RIC hearing aid and tested with 5 receiver size conditions. Measured occlusion effect was calculated from aided and unaided real-ear responses obtained while subjects vocalized /i/. Perceived occlusion measures were acquired using an occlusion effect scale.

Results
Measured occlusion was greatest for the largest receiver. The most common perceived occlusion ratings were none to mild occlusion for all receiver sizes. Perceived ratings were weakly correlated to acoustic measures. There was little to no correlation between receiver size and estimated ear canal volume.

Conclusions
Measured and perceived occlusion was minor in all receiver conditions. Occlusion was not correlated to ear canal volume, suggesting that RIC hearing aids most often result in negligible amounts of measured and perceived occlusion effect, regardless of ear canal size. Because no significant relationship existed between the occlusion measures, clinicians may need to consider that self-rating of occlusion may not match measured occlusion results.
Comparing Pure-, Pulsed, and Warbled Tone Thresholds in Adults at 3000 and 6000 Hz
Authors: Franklin Clifford A. , Franklin Thomas C. , Franklin Jennifer L. 
Published: June 2011

Purpose
Pulsed and warbled tones are suitable substitutions for pure tones in hearing threshold measurement according to the 2005 American Speech-Language-Hearing Association guidelines. These guidelines also recommend measuring thresholds at 3000 and 6000 Hz. To date, there is no research directly supporting substitution of pulsed or warbled tones for pure tones at 3000 and 6000 Hz for listeners with normal hearing or with hearing loss. This study compared pure-, pulsed, and warbled tone thresholds at 3000 and 6000 Hz.

Method
Forty-seven adults with normal hearing and 16 adults with sensorineural hearing loss participated in this study. Air-conduction thresholds were elicited with pure tones at octave intervals from 250 to 8000 Hz and with pure-, pulsed, and warbled tone stimuli at 3000 and 6000 Hz.

Results
Small mean differences in thresholds were obtained using each of the 3 stimulus types for both listeners with normal hearing and hearing loss. Some of the mean differences tested were found to be statistically significant. The differences were nevertheless small and in all cases within the clinically accepted 5-dB step size.

Conclusion
Although substitutions did not violate the 5-dB step size, the slope of a listener’s hearing loss may be a factor in the inaccuracy of measurement during the substitution of warbled tones for pure tones.
Targeting Hearing Health Messages for Users of Personal Listening Devices
Authors: Punch Jerry L. , Elfenbein Jill L. , James Richard R. 
Published: June 2011

Purpose
To summarize the literature on patterns and risks of personal listening device (PLD) use, which is ubiquitous among teenagers and young adults. The review emphasizes risk awareness, health concerns of PLD users, inclination to take actions to prevent hearing loss from exposure to loud music, and specific instructional messages that are likely to motivate such preventive actions.

Method
We conducted a systematic, critical review of the English-language scholarly literature on the topic of PLDs and their potential effects on human hearing. We used popular database search engines to locate relevant professional journals, books, recent conference papers, and other reference sources.

Conclusions
Adolescents and young adults appear to have somewhat different perspectives on risks to hearing posed by PLD use. Messages designed to suggest actions they might take in avoiding or reducing these risks, therefore, need to be targeted to achieve optimal outcomes. We offer specific recommendations regarding the framing and content of educational messages that are most likely to be effective in reducing the potentially harmful effects of loud music on hearing in these populations, and we note future research needs.
Abrupt Holocene climate change as an important factor for human migration in West Greenland
Authors: D’Andrea William J. , Huang Yongsong , Fritz Sherilyn C. , Anderson N. John 
Published: June 2011

West Greenland has had multiple episodes of human colonization and cultural transitions over the past 4,500 y. However, the explanations for these large-scale human migrations are varied, including climatic factors, resistance to adaptation, economic marginalization, mercantile exploration, and hostile neighborhood interactions. Evaluating the potential role of climate change is complicated by the lack of quantitative paleoclimate reconstructions near settlement areas and by the relative stability of Holocene temperature derived from ice cores atop the Greenland ice sheet. Here we present high-resolution records of temperature over the past 5,600 y based on alkenone unsaturation in sediments of two lakes in West Greenland. We find that major temperature changes in the past 4,500 y occurred abruptly (within decades), and were coeval in timing with the archaeological records of settlement and abandonment of the Saqqaq, Dorset, and Norse cultures, which suggests that abrupt temperature changes profoundly impacted human civilization in the region. Temperature variations in West Greenland display an antiphased relationship to temperature changes in Ireland over centennial to millennial timescales, resembling the interannual to multidecadal temperature seesaw associated with the North Atlantic Oscillation.
Enhanced chemistry-climate feedbacks in past greenhouse worlds
Authors: Beerling David J. , Fox Andrew , Stevenson David S. , Valdes Paul J. 
Published: June 2011

Trace greenhouse gases are a fundamentally important component of Earth’s global climate system sensitive to global change. However, their concentration in the pre-Pleistocene atmosphere during past warm greenhouse climates is highly uncertain because we lack suitable geochemical or biological proxies. This long-standing issue hinders assessment of their contribution to past global warmth and the equilibrium climate sensitivity of the Earth system (Ess) to CO2. Here we report results from a series of three-dimensional Earth system modeling simulations indicating that the greenhouse worlds of the early Eocene (55 Ma) and late Cretaceous (90 Ma) maintained high concentrations of methane, tropospheric ozone, and nitrous oxide. Modeled methane concentrations were four- to fivefold higher than the preindustrial value typically adopted in modeling investigations of these intervals, even after accounting for the possible high CO2-suppression of biogenic isoprene emissions on hydroxyl radical abundance. Higher concentrations of trace greenhouse gases exerted marked planetary heating (> 2 K), amplified in the high latitudes (> 6 K) by lower surface albedo feedbacks, and increasedEssin the Eocene by 1 K. Our analyses indicate the requirement for including non-CO2greenhouse gases in model-basedEssestimates for comparison with empirical paleoclimate assessments, and point to chemistry-climate feedbacks as possible amplifiers of climate sensitivity in the Anthropocene.
Structure of transcription factor HetR required for heterocyst differentiation in cyanobacteria
Authors: Kim Youngchang , Joachimiak Grazyna , Ye Zi , Binkowski T. Andrew , Zhang Rongguang , Gornicki Piotr , Callahan Sean M. , Hess Wolfgang R. , Haselkorn Robert , Joachimiak Andrzej 
Published: June 2011

HetR is an essential regulator of heterocyst development in cyanobacteria. HetR binds to a DNA palindrome upstream of the
hetP
gene. We report the crystal structure of HetR from
Fischerella
at 3.0 Å. The protein is a dimer comprised of a central DNA-binding unit containing the N-terminal regions of the two subunits organized with two helix-turn-helix motifs; two globular flaps extending in opposite directions; and a hood over the central core formed from the C-terminal subdomains. The flaps and hood have no structural precedent in the protein database, therefore representing new folds. The structural assignments are supported by site-directed mutagenesis and DNA-binding studies. We suggest that HetR serves as a scaffold for assembly of transcription components critical for heterocyst development.
Replication enhancer elements within the open reading frame of tick-borne encephalitis virus and their evolution within the Flavivirus genus
Authors: Tuplin A. , Evans D. J. , Buckley A. , Jones I. M. , Gould E. A. , Gritsun T. S. 
Published: May 2011

AbstractWe provide experimental evidence of a replication enhancer element (REE) within the capsid gene of tick-borne encephalitis virus (TBEV, genus Flavivirus). Thermodynamic and phylogenetic analyses predicted that the REE folds as a long stable stem–loop (designated SL6), conserved among all tick-borne flaviviruses (TBFV). Homologous sequences and potential base pairing were found in the corresponding regions of mosquito-borne flaviviruses, but not in more genetically distant flaviviruses. To investigate the role of SL6, nucleotide substitutions were introduced which changed a conserved hexanucleotide motif, the conformation of the terminal loop and the base-paired dsRNA stacking. Substitutions were made within a TBEV reverse genetic system and recovered mutants were compared for plaque morphology, single-step replication kinetics and cytopathic effect. The greatest phenotypic changes were observed in mutants with a destabilized stem. Point mutations in the conserved hexanucleotide motif of the terminal loop caused moderate virus attenuation. However, all mutants eventually reached the titre of wild-type virus late post-infection. Thus, although not essential for growth in tissue culture, the SL6 REE acts to up-regulate virus replication. We hypothesize that this modulatory role may be important for TBEV survival in nature, where the virus circulates by non-viraemic transmission between infected and non-infected ticks, during co-feeding on local rodents.
Mechanisms of Lipotoxicity in NAFLD and Clinical Implications
Authors: Ibrahim Samar H. , Kohli Rohit , Gores Gregory J. 
Published: June 2011

ABSTRACTWith the epidemic of childhood obesity, nonalcoholic fatty liver disease (NAFLD) has become the most common cause of chronic liver disease in pediatrics. NAFLD is strongly associated with insulin resistance and increased level of serum free fatty acids (FFAs). FFAs have direct hepatotoxicity through the induction of an endoplasmic reticulum stress response and subsequently activation of the mitochondrial pathway of cell death. FFAs may also result in lysosomal dysfunction and alter death receptor gene expression. Lipoapoptosis is a key pathogenic process in NAFLD, and correlates with progressive inflammation, and fibrosis. Accumulation of triglyceride in the liver results from uptake and esterification of FFAs by the hepatocyte, and is less likely to be hepatotoxic per se. To date, there are no proven effective therapies that halt NAFLD progression or unfortunately improve prognosis in children. The cellular mechanisms of lipotoxicity are complex but provide potential therapeutic targets for NAFLD. In this review we discuss several potential therapeutic opportunities in detail including inhibition of apoptosis, c‐Jun‐N‐terminal kinase, and endoplasmic reticulum stress pathways.
From IMGT-ONTOLOGY DESCRIPTION Axiom to IMGT Standardized Labels: For Immunoglobulin (IG) and T Cell Receptor (TR) Sequences and Structures
Authors: Lefranc Marie-Paule 
Published: June 2011

INTRODUCTIONMore than 560 IMGT standardized labels have been defined for the description of immunoglobulin (IG) and T cell receptor (TR) sequences and structures. These labels, as detailed here, are based on the concepts of description (generated from the DESCRIPTION axiom) of IMGT-ONTOLOGY, the global reference in immunogenetics and immunoinformatics, built by IMGT, the international ImMunoGeneTics information system. IMGT labels for nucleotide sequences correspond to the “Molecule_EntityPrototype” concept with its leafconcepts (a leafconcept is the finest level of granularity), its associated concepts of description, and its prototypes or graphical representations. These labels have been essential for the IG and TR description in the IMGT sequence and gene databases (IMGT/LIGM-DB, IMGT/GENE-DB) and tools (IMGT/V-QUEST, IMGT/JunctionAnalysis, IMGT/HighV-QUEST, IMGT/LIGMotif). IMGT labels for amino acid sequences and structures correspond to the “RECEPTOR,” “CHAIN,” and “DOMAIN” concepts. These labels have been crucial for the IG and TR description in the IMGT two-dimensional (2D) and three-dimensional (3D) databases (IMGT/2Dstructure-DB, IMGT/3Dstructure-DB) and tools (IMGT/DomainDisplay, IMGT/DomainGapAlign). As all leafconcepts of description are directly translated into IMGT standardized labels for use in the IMGT databases and tools, IMGT-ONTOLOGY concepts of description contribute to data coherence and consistency and facilitate the interoperability between the different components of IMGT, bridging the description of sequences and structures.
IMGT Collier de Perles for the Variable (V), Constant (C), and Groove (G) Domains of IG, TR, MH, IgSF, and MhSF
Authors: Lefranc Marie-Paule 
Published: June 2011

INTRODUCTIONThe “IMGT Collier de Perles” (or “IMGT_Collier_de_Perles”) concept is a major concept of numerotation (generated from the NUMEROTATION axiom) of IMGT-ONTOLOGY, the global reference in immunogenetics and immunoinformatics, built by IMGT, the international ImMunoGeneTics information system. The “IMGT Collier de Perles” concept, described here, allows standardized two-dimensional (2D) graphical representations of the domains, based on the IMGT unique numbering. Three leafconcepts (a leafconcept is a concept that corresponds to the finest level of granularity) have been defined: for the variable (V) domain and constant (C) domain of the immunoglobulin superfamily (IgSF) and for the groove (G) domain of the major histocompatibility (MH) superfamily (MhSF). IMGT Colliers de Perles are obtained, starting from V, C, or G domain amino acid sequences, using IMGT/DomainGapAlign and IMGT/Collier de Perles tools. In IMGT/3Dstructure-DB, IMGT Colliers de Perles of V and C domains are provided with hydrogen bonds and those of G domains with IMGT pMH contact analysis. IMGT Colliers de Perles allows one to bridge the gap between sequences and three-dimensional (3D) structures, whatever the species, the IgSF or MhSF protein, or the chain type. They are particularly useful for antibody engineering, sequence-structure analysis, visualization and comparison of positions for mutations, polymorphisms and contact analysis of immunoglobulins (IG), T cell receptors (TR), MH, and related proteins of the immune system (RPI) belonging to the IgSF and MhSF.
Dissection and Staining of Drosophila Optic Lobes at Different Stages of Development
Authors: Morante Javier , Desplan Claude 
Published: June 2011

INTRODUCTIONThe Drosophila visual system is composed of the retina and the optic lobes, which are the ganglia where photoreceptors project and initial processing of visual inputs occur. This protocol outlines procedures for dissecting the optic lobes from Drosophila larvae, pupae, and adults. It also describes methods for visualizing the anatomy of brain neural circuits by staining with fluorescent secondary antibodies and primary antibodies specific for various neuronal populations and architectural features.
IMGT/JunctionAnalysis: IMGT Standardized Analysis of the V-J and V-D-J Junctions of the Rearranged Immunoglobulins (IG) and T Cell Receptors (TR)
Authors: Giudicelli Véronique , Lefranc Marie-Paule 
Published: June 2011

INTRODUCTIONIMGT/JunctionAnalysis is the online IMGT tool for the detailed and standardized analysis of the junctions between the variable (V), diversity (D), and joining (J) genes (V-J and V-D-J junctions) of the rearranged immunoglobulin (IG) or antibody and T cell receptor (TR) variable domains. The V-(D)-J junctions comprise the rearranged CDR3-IMGT and its anchors 2nd-CYS 104 and J-PHE or J-TRP 118. The diversity of the junctions that determines the antigen receptor specificity results from complex molecular mechanisms that occur at the DNA level during the IG and TR synthesis and create combinatorial diversity, N-diversity and, for IG, somatic hypermutations. The annotation of V-J or V-D-J junctions in rearranged IG and TR sequences represents a huge challenge due to its uniqueness and complexity. IMGT/JunctionAnalysis has been a major breakthrough by providing, for the first time, a very detailed and accurate analysis of the junctions. The tool, whose use is described here, identifies the D genes in the IGH, TRB, and TRD junctions, the trimmed nucleotides (nt) at the end of the genes which recombine, and the palindromic P regions in the absence of gene trimming. It delimits the N regions that result from the N-diversity, calculates the ratio of G+C nucleotides in the N regions, and evaluates the number of somatic hypermutations for each gene within the junction.
IMGT/Collier de Perles: IMGT Standardized Representation of Domains (IG, TR, and IgSF Variable and Constant Domains, MH and MhSF Groove Domains)
Authors: Ehrenmann François , Giudicelli Véronique , Duroux Patrice , Lefranc Marie-Paule 
Published: June 2011

INTRODUCTIONIMGT/Collier de Perles is the IMGT online tool that allows one to draw standardized IMGT two-dimensional (2D) graphical representations of protein domains, or IMGT Colliers de Perles, starting from the user’s own domain amino acid (AA) sequences. The use of this tool is described here. IMGT Colliers de Perles can be drawn for three domain types: the variable (V) domain and constant (C) domain of the immunoglobulin (IG) and T cell receptor (TR) and other members of the immunoglobulin superfamily (IgSF), and the groove (G) domain of the major histocompatibility (MH) and other members of the MH superfamily (MhSF). Sequences have to be gapped according to the IMGT unique numbering, using, for example, IMGT/DomainGapAlign. Resulting IMGT Colliers de Perles allow one to quickly visualize amino acids, which are important for the three-dimensional (3D) structural configuration, and to delimit the standardized framework regions (FR-IMGT) and complementarity determining regions (CDR-IMGT) of the IG and TR V-DOMAIN. The length of the strands, loops, and turns and, for the G type, the length of the helix represented in IMGT Colliers de Perles become crucial information in the domain characterization.