bluuebunny/crossref_metadata_2025_split huggingface dataset:
Food and beverage choices contributing to dietary guidelines adherence in the Lower Mississippi Delta
Authors: Thomson Jessica L , Onufrak Stephen J , Connell Carol L , Zoellner Jamie M , Tussing-Humphreys Lisa M , Bogle Margaret L , Yadrick Kathy 
Published: June 2011

AbstractObjectivesThe objectives of the present study were to evaluate diet quality among Lower Mississippi Delta (LMD) residents using the Healthy Eating Index-2005 (HEI-2005) and to identify the top five dietary sources contributing to HEI-2005 components. Demographic differences in HEI-2005 scores were also explored.DesignDiet quality was evaluated using HEI-2005. Demographic differences in HEI-2005 scores were investigated using multivariable regression models adjusting for multiple comparisons. The top five dietary sources contributing to HEI-2005 components were identified by estimating and ranking mean MyPyramid equivalents overall and by demographic characteristics.SettingDietary data, based on a single 24 h recall, from the Foods of Our Delta Study 2000 (FOODS 2000) were used in the analyses.SubjectsFOODS 2000 adult participants 18 years of age or older.ResultsYounger age was the largest determinant of low diet quality in the LMD with HEI-2005 total and seven component scores declining with decreasing age. Income was not a significant factor for HEI-2005 total or component scores. The top five dietary sources differed by all five of the demographic variables, particularly for total vegetables and energy from solid fats, alcoholic beverages and added sugars (SoFAAS). Soft drinks were the leading source of SoFAAS energy intake for all demographic groups.ConclusionsThe assessment of diet quality and identification of top dietary sources revealed the presence of demographic differences for selected HEI-2005 components. These findings allow identification of food patterns and culturally appropriate messaging and highlight the difficulties of treating this region as a homogeneous population.
Relating weight constraint and aggregate programs: Semantics and representation
Authors: LIU GUOHUA , YOU JIA-HUAI 
Published: June 2011

AbstractWeight constraint and aggregate programs are among the most widely used logic programs with constraints. In this paper, we relate the semantics of these two classes of programs, namely, the stable model semantics for weight constraint programs and the answer set semantics based on conditional satisfaction for aggregate programs. Both classes of programs are instances of logic programs with constraints, and in particular, the answer set semantics for aggregate programs can be applied to weight constraint programs. We show that the two semantics are closely related. First, we show that for a broad class of weight constraint programs, called strongly satisfiable programs, the two semantics coincide. When they disagree, a stable model admitted by the stable model semantics may be circularly justified. We show that the gap between the two semantics can be closed by transforming a weight constraint program to a strongly satisfiable one so that no circular models may be generated under the current implementation of the stable model semantics. We further demonstrate the close relationship between the two semantics by formulating a transformation from weight constraint programs to logic programs with nested expressions, which preserves the answer set semantics. Our study on the semantics leads to an investigation of a methodological issue, namely, the possibility of compact representation of aggregate programs by weight constraint programs. We show that almost all standard aggregates can be encoded by weight constraints compactly. This makes it possible to compute the answer sets of aggregate programs using the answer set programming solvers for weight constraint programs. This approach is compared experimentally with the ones where aggregates are handled more explicitly, which show that the weight constraint encoding of aggregates enables a competitive approach to answer set computation for aggregate programs.
Community genomic analysis of an extremely acidophilic sulfur-oxidizing biofilm
Authors: Jones Daniel S , Albrecht Heidi L , Dawson Katherine S , Schaperdoth Irene , Freeman Katherine H , Pi Yundan , Pearson Ann , Macalady Jennifer L 
Published: June 2011

Abstract
Highly acidic (pH 0–1) biofilms, known as ‘snottites’, form on the walls and ceilings of hydrogen sulfide-rich caves. We investigated the population structure, physiology and biogeochemistry of these biofilms using metagenomics, rRNA methods and lipid geochemistry. Snottites from the Frasassi cave system (Italy) are dominated (&gt;70% of cells) by Acidithiobacillus thiooxidans, with smaller populations including an archaeon in the uncultivated ‘G-plasma’ clade of Thermoplasmatales (&gt;15%) and a bacterium in the Acidimicrobiaceae family (&gt;5%). Based on metagenomic evidence, the Acidithiobacillus population is autotrophic (ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), carboxysomes) and oxidizes sulfur by the sulfide–quinone reductase and sox pathways. No reads matching nitrogen fixation genes were detected in the metagenome, whereas multiple matches to nitrogen assimilation functions are present, consistent with geochemical evidence, that fixed nitrogen is available in the snottite environment to support autotrophic growth. Evidence for adaptations to extreme acidity include Acidithiobacillus sequences for cation transporters and hopanoid synthesis, and direct measurements of hopanoid membrane lipids. Based on combined metagenomic, molecular and geochemical evidence, we suggest that Acidithiobacillus is the snottite architect and main primary producer, and that snottite morphology and distributions in the cave environment are directly related to the supply of C, N and energy substrates from the cave atmosphere.
De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities
Authors: Narasingarao Priya , Podell Sheila , Ugalde Juan A , Brochier-Armanet Céline , Emerson Joanne B , Brocks Jochen J , Heidelberg Karla B , Banfield Jillian F , Allen Eric E 
Published: June 2011

Abstract
This study describes reconstruction of two highly unusual archaeal genomes by de novo metagenomic assembly of multiple, deeply sequenced libraries from surface waters of Lake Tyrrell (LT), a hypersaline lake in NW Victoria, Australia. Lineage-specific probes were designed using the assembled genomes to visualize these novel archaea, which were highly abundant in the 0.1–0.8 μm size fraction of lake water samples. Gene content and inferred metabolic capabilities were highly dissimilar to all previously identified hypersaline microbial species. Distinctive characteristics included unique amino acid composition, absence of Gvp gas vesicle proteins, atypical archaeal metabolic pathways and unusually small cell size (approximately 0.6 μm diameter). Multi-locus phylogenetic analyses demonstrated that these organisms belong to a new major euryarchaeal lineage, distantly related to halophilic archaea of class Halobacteria. Consistent with these findings, we propose creation of a new archaeal class, provisionally named ‘Nanohaloarchaea’. In addition to their high abundance in LT surface waters, we report the prevalence of Nanohaloarchaea in other hypersaline environments worldwide. The simultaneous discovery and genome sequencing of a novel yet ubiquitous lineage of uncultivated microorganisms demonstrates that even historically well-characterized environments can reveal unexpected diversity when analyzed by metagenomics, and advances our understanding of the ecology of hypersaline environments and the evolutionary history of the archaea.
Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys
Authors: Werner Jeffrey J , Koren Omry , Hugenholtz Philip , DeSantis Todd Z , Walters William A , Caporaso J Gregory , Angenent Largus T , Knight Rob , Ley Ruth E 
Published: June 2011

Abstract
Taxonomic classification of the thousands–millions of 16S rRNA gene sequences generated in microbiome studies is often achieved using a naïve Bayesian classifier (for example, the Ribosomal Database Project II (RDP) classifier), due to favorable trade-offs among automation, speed and accuracy. The resulting classification depends on the reference sequences and taxonomic hierarchy used to train the model; although the influence of primer sets and classification algorithms have been explored in detail, the influence of training set has not been characterized. We compared classification results obtained using three different publicly available databases as training sets, applied to five different bacterial 16S rRNA gene pyrosequencing data sets generated (from human body, mouse gut, python gut, soil and anaerobic digester samples). We observed numerous advantages to using the largest, most diverse training set available, that we constructed from the Greengenes (GG) bacterial/archaeal 16S rRNA gene sequence database and the latest GG taxonomy. Phylogenetic clusters of previously unclassified experimental sequences were identified with notable improvements (for example, 50% reduction in reads unclassified at the phylum level in mouse gut, soil and anaerobic digester samples), especially for phylotypes belonging to specific phyla (Tenericutes, Chloroflexi, Synergistetes and Candidate phyla TM6, TM7). Trimming the reference sequences to the primer region resulted in systematic improvements in classification depth, and greatest gains at higher confidence thresholds. Phylotypes unclassified at the genus level represented a greater proportion of the total community variation than classified operational taxonomic units in mouse gut and anaerobic digester samples, underscoring the need for greater diversity in existing reference databases.
High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton
Authors: Martinez-Garcia Manuel , Swan Brandon K , Poulton Nicole J , Gomez Monica Lluesma , Masland Dashiell , Sieracki Michael E , Stepanauskas Ramunas 
Published: June 2011

Abstract
Recent discoveries suggest that photoheterotrophs (rhodopsin-containing bacteria (RBs) and aerobic anoxygenic phototrophs (AAPs)) and chemoautotrophs may be significant for marine and freshwater ecosystem productivity. However, their abundance and taxonomic identities remain largely unknown. We used a combination of single-cell and metagenomic DNA sequencing to study the predominant photoheterotrophs and chemoautotrophs inhabiting the euphotic zone of temperate, physicochemically diverse freshwater lakes. Multi-locus sequencing of 712 single amplified genomes, generated by fluorescence-activated cell sorting and whole genome multiple displacement amplification, showed that most of the cosmopolitan freshwater clusters contain photoheterotrophs. These comprised at least 10–23% of bacterioplankton, and RBs were the dominant fraction. Our data demonstrate that Actinobacteria, including clusters acI, Luna and acSTL, are the predominant freshwater RBs. We significantly broaden the known taxonomic range of freshwater RBs, to include Alpha-, Beta-, Gamma- and Deltaproteobacteria, Verrucomicrobia and Sphingobacteria. By sequencing single cells, we found evidence for inter-phyla horizontal gene transfer and recombination of rhodopsin genes and identified specific taxonomic groups involved in these evolutionary processes. Our data suggest that members of the ubiquitous betaproteobacteria Polynucleobacter spp. are the dominant AAPs in temperate freshwater lakes. Furthermore, the RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) gene was found in several single cells of Betaproteobacteria, Bacteroidetes and Gammaproteobacteria, suggesting that chemoautotrophs may be more prevalent among aerobic bacterioplankton than previously thought. This study demonstrates the power of single-cell DNA sequencing addressing previously unresolved questions about the metabolic potential and evolutionary histories of uncultured microorganisms, which dominate most natural environments.
Localization of electrons due to orbitally ordered bi-stripes in the bilayer manganite La

2-2
x

Sr

1+2
x

Mn
2
O
7
(
x
∼ 0.59)
Authors: Sun Z. , Wang Q. , Fedorov A. V. , Zheng H. , Mitchell J. F. , Dessau D. S. 
Published: June 2011

Electronic phases with stripe patterns have been intensively investigated for their vital roles in unique properties of correlated electronic materials. How these real-space patterns affect the conductivity and other properties of materials (which are usually described in momentum space) is one of the major challenges of modern condensed matter physics. By studying the electronic structure of La

2-2
x

Sr

1+2
x

Mn
2
O
7
(
x
∼ 0.59) and in combination with earlier scattering measurements, we demonstrate the variation of electronic properties accompanying the melting of so-called bi-stripes in this material. The static bi-stripes can strongly localize the electrons in the insulating phase above
T

c

∼ 160 K, while the fraction of mobile electrons grows, coexisting with a significant portion of localized electrons when the static bi-stripes melt below
T

c

. The presence of localized electrons below
T

c

suggests that the melting bi-stripes exist as a disordered or fluctuating counterpart. From static to melting, the bi-stripes act as an atomic-scale electronic valve, leading to a “colossal” metal-insulator transition in this material.
Use of Recombinant Factor VIIa in Patients with Amniotic Fluid Embolism
Authors: Leighton Barbara L. , Wall Michael H. , Lockhart Ellen M. , Phillips Louise E. , Zatta Amanda J. 
Published: June 2011

Background
Patients with amniotic fluid embolism (AFE) (major cardiac and pulmonary symptoms plus consumptive coagulopathy) have high circulating tissue factor concentrations. Recombinant factor VIIa (rVIIa) has been used to treat hemorrhage in AFE patients even though rVIIa can combine with circulating tissue factor and form intravascular clots. A systematic review was done of case reports from 2003 to 2009 of AFE patients with massive hemorrhage who were and were not treated with rVIIa to assess the thrombotic complication risk.

Methods
MEDLINE was searched for case reports of AFE patients receiving rVIIa (rVIIa cases) and of AFE patients who received surgery to control bleeding but no rVIIa (cohorts who did not receive rVIIa). Additional AFE case reports were obtained from the Food and Drug Administration, the Australian and New Zealand Haemostasis Registry, and scientific meeting abstracts. The risk of a negative outcome (permanent disability or death) in rVIIa cases versus cohorts who did not receive rVIIa was calculated using risk ratio and 95% confidence interval.

Results
Sixteen rVIIa cases and 28 cohorts were identified who did not receive rVIIa. All patients had surgery to control bleeding. Death, permanent disability, and full recovery occurred in 8, 6, and 2 rVIIa cases and 7, 4, and 17 cohorts who did not receive rVIIa (risk ratio 2.2, 95% CI 1.4-3.7 for death or permanent disability vs. full recovery).

Conclusion
Recombinant factor VIIa cases had significantly worse outcomes than cohorts who did not receive rVIIa. It is recommended that rVIIa be used in AFE patients only when the hemorrhage cannot be stopped by massive blood component replacement.
Estimating Anesthesia Time Using the Medicare Claim
Authors: Silber Jeffrey H. , Rosenbaum Paul R. , Even-Shoshan Orit , Mi Lanyu , Kyle Fabienne A. , Teng Yun , Bratzler Dale W. , Fleisher Lee A. 
Published: June 2011

Introduction
Procedure length is a fundamental variable associated with quality of care, though seldom studied on a large scale. The authors sought to estimate procedure length through information obtained in the anesthesia claim submitted to Medicare to validate this method for future studies.

Methods
The Obesity and Surgical Outcomes Study enlisted 47 hospitals located across New York, Texas, and Illinois to study patients undergoing hip, knee, colon, and thoracotomy procedures. A total of 15,914 charts were abstracted to determine body mass index and initial patient physiology. Included in this abstraction were induction, cut, close, and recovery room times. This chart information was merged to Medicare claims that included anesthesia Part B billing information. Correlations between chart times and claim times were analyzed, models developed, and median absolute differences in minutes calculated.

Results
Of the 15,914 eligible patients, there were 14,369 for whom both chart and claim times were available for analysis. For these 14,369, the Spearman correlation between chart and claim time was 0.94 (95% CI 0.94, 0.95), and the median absolute difference between chart and claim time was only 5 min (95% CI: 5.0, 5.5). The anesthesia claim can also be used to estimate surgical procedure length, with only a modest increase in error.

Conclusion
The anesthesia bill found in Medicare claims provides an excellent source of information for studying surgery time on a vast scale throughout the United States. However, errors in both chart abstraction and anesthesia claims can occur. Care must be taken in the handling of outliers in these data.
Neural Correlates of Chronic Low Back Pain Measured by Arterial Spin Labeling
Authors: Wasan Ajay D. , Loggia Marco L. , Chen Li Q. , Napadow Vitaly , Kong Jian , Gollub Randy L. 
Published: June 2011

Background
The varying nature of chronic pain (CP) is difficult to correlate to neural activity using typical functional magnetic resonance imaging methods. Arterial spin labeling is a perfusion-based imaging technique allowing the absolute quantification of regional cerebral blood flow, which is a surrogate measure of neuronal activity.

Methods
Subjects with chronic low back and radicular pain and matched healthy normal subjects, undergoing identical procedures, participated in three sessions: a characterization and training session and two arterial spin labeling sessions. In the first imaging session, CP (if any) was exacerbated using clinical maneuvers; in the second session, noxious heat was applied to the affected leg dermatome, the intensity of which was matched to the pain intensity level of the CP exacerbations for each back pain subject.

Results
The clinically significant worsening of ongoing CP (≤ 30%, n = 16) was associated with significant regional blood flow increases (6-10 mm/100 g of tissue/min, P less than 0.01) within brain regions known to activate with experimental pain (somatosensory, prefrontal, and insular cortices) and in other structures observed less frequently in experimental pain studies, such as the superior parietal lobule (part of the dorsal attention network). This effect is specific to changes in ongoing CP as it is observed during worsening CP, but it is not observed after thermal pain application, or in matched, pain-free healthy controls.

Conclusions
Study findings demonstrate the use of arterial spin labeling to investigate the neural processing of CP, and these findings are a step forward in the quest for objective biomarkers of the chronic pain experience.
Coeliac Disease Diagnosis
Authors: Ribes‐Koninckx C. , Mearin ML. , Korponay‐Szabó IR. , Shamir R. , Husby S. , Ventura A. , Branski D. , Catassi C. , Koletzko S. , Mäki M. , Troncone R. , Zimmer KP. ,   ESPGHAN Working Group on Coeliac Disease Diagnosis
Published: June 2011

ABSTRACTBackground and Objectives:A revision of criteria for diagnosing coeliac disease (CD) is being conducted by The European Society for Pediatric Gastroenterology, Hepatology, and Nutrition (ESPGHAN). In parallel, we have performed a survey aimed to evaluate present practices for CD among paediatric gastroenterologists and to learn their views on the need for modification of present criteria for CD diagnosis.Patients and Methods:Questionnaires were distributed to experienced paediatric gastroenterologists (ESPGHAN members) via the Internet.Results:Overall, 95 valid questionnaires were available for analysis, pertaining to 28 different countries, with the majority of responders treating patients with CD for >15 years. Only about 12% of the responders comply with present criteria, noncompliance being related mainly to the challenge policy. Approximately 90% request a revision and modification of the present criteria. Forty‐four percent want to omit the small bowel biopsy in symptomatic children with positive anti‐tissue transglutaminase immunoglobulin (Ig) A or endomysial IgA antibodies, especially if they are DQ2/DQ8 positive. For silent cases detected by screening with convincingly positive anti‐tissue transglutaminase IgA or EMA IgA, about 30% consider that no small bowel biopsy should be required in selected cases. Adding human leukocyte antigen typing in the diagnostic workup was asked for by 42% of the responders. As for gluten challenge, a new policy is advocated restricting its obligation to cases whenever the diagnosis is doubtful or unclear.Conclusions:Based on these opinions, revision of the ESPGHAN criteria for diagnosing CD is urgently needed.
Pharmacokinetics and Safety of Dexlansoprazole MR in Adolescents With Symptomatic GERD
Authors: Kukulka Michael , Wu Jingtao , Perez Maria Claudia 
Published: June 2011

ABSTRACTObjectives:Dexlansoprazole MR 30 mg once daily (QD) is approved in adults for the treatment of symptomatic nonerosive gastroesophageal reflux disease (GERD) and maintenance of healed erosive esophagitis (EE); 60 mg is approved for healing EE. The present study assesses the pharmacokinetic (PK) profile and safety of dexlansoprazole MR in adolescent patients.Patients and Methods:Phase 1, open‐label, parallel‐group, multicenter study in male and female adolescents (12–17 years) with GERD. Patients were randomized to receive dexlansoprazole MR (30 or 60 mg, QD) for 7 days. Blood samples to determine dexlansoprazole plasma concentrations were drawn over a 24‐hour period after dosing on day 7. Dexlansoprazole plasma concentrations and PK parameters were summarized by dose group. Safety assessments included monitoring of adverse events (AEs).Results:Thirty‐six patients (mean age 14.6 years), 14 boys and 22 girls, were randomized, with PK data available for 35 patients. The overall exposure of dexlansoprazole after administration of the 60‐mg capsule was slightly less than double the exposure from the 30‐mg capsule. Cmax (691 and 1136 ng/mL) and area under the plasma concentration time curve (2886 and 5120 ng · h/mL) values for the 30‐ and 60‐mg doses, respectively, were similar to results from previous phase 1 studies in healthy adults. Twelve of 36 patients (33.3%) experienced a total of 21 treatment‐emergent AEs. All of the AEs were considered to be of mild severity.Conclusions:The PK data for dexlansoprazole MR 30‐ and 60‐mg capsules in adolescent patients with symptomatic GERD were similar to those in healthy adults. Both doses were well tolerated.