bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of the Glidescope® and Pentax AWS®laryngoscopes to the Macintosh laryngoscope for use by Advanced Paramedics in easy and simulated difficult intubation
Authors: Nasim Sajid , Maharaj Chrisen H , Malik Muhammad A , O' Donnell John , Higgins Brendan D , Laffey John G 
Published: May 2009

Abstract

Background
Intubation of the trachea in the pre-hospital setting may be lifesaving in severely ill and injured patients. However, tracheal intubation is frequently difficult to perform in this challenging environment, is associated with a lower success rate, and failed tracheal intubation constitutes an important cause of morbidity. Novel indirect laryngoscopes, such as the Glidescope® and the AWS® laryngoscopes may reduce this risk.

Methods
We compared the efficacy of these devices to the Macintosh laryngoscope when used by 25 Advanced Paramedics proficient in direct laryngoscopy, in a randomized, controlled, manikin study. Following brief didactic instruction with the Glidescope® and the AWS® laryngoscopes, each participant took turns performing laryngoscopy and intubation with each device, in an easy intubation scenario and following placement of a hard cervical collar, in a SimMan® manikin.

Results
Both the Glidescope® and the AWS® performed better than the Macintosh, and demonstrate considerable promise in this context. The AWS® had the least number of dental compressions in all three scenarios, and in the cervical spine immobilization scenario it required fewer maneuvers to optimize the view of the glottis.

Conclusion
The Glidescope® and AWS® devices possess advantages over the conventional Macintosh laryngoscope when used by Advanced Paramedics in normal and simulated difficult intubation scenarios in this manikin study. Further studies are required to extend these findings to the clinical setting.
Food allergy alters jejunal circular muscle contractility and induces local inflammatory cytokine expression in a mouse model
Authors: Valeur Jørgen , Lappalainen Jani , Rita Hannu , Lin Aung Htun , Kovanen Petri T , Berstad Arnold , Eklund Kari K , Vaali Kirsi 
Published: May 2009

Abstract

Background
We hypothesized that food allergy causes a state of non-specific jejunal dysmotility. This was tested in a mouse model.

Methods
Balb/c mice were epicutaneously sensitized with ovalbumin and challenged with 10 intragastric ovalbumin administrations every second day. Smooth muscle contractility of isolated circular jejunal sections was studied in organ bath with increasing concentrations of carbamylcholine chloride (carbachol). Smooth muscle layer thickness and mast cell protease-1 (MMCP-1) positive cell density were assayed histologically. Serum MMCP-1 and immunoglobulins were quantified by ELISA, and mRNA expressions of IFN-γ, IL-4, IL-6 and TGFβ-1 from jejunal and ileal tissue segments were analyzed with quantitative real-time PCR.

Results
Ovalbumin-specific serum IgE correlated with jejunal MMCP-1+ cell density. In the allergic mice, higher concentrations of carbachol were required to reach submaximal muscular stimulation, particularly in preparations derived from mice with diarrhoea. Decreased sensitivity to carbachol was associated with increased expression of IL-4 and IL-6 mRNA in jejunum. Smooth muscle layer thickness, as well as mRNA of IFN-γ and TGF-β1 remained unchanged.

Conclusion
In this mouse model of food allergy, we demonstrated a decreased response to a muscarinic agonist, and increased levels of proinflammatory IL-6 and Th2-related IL-4, but not Th1-related IFN-γ mRNAs in jejunum. IgE levels in serum correlated with the number of jejunal MMCP-1+ cells, and predicted diarrhoea. Overall, these changes may reflect a protective mechanism of the gut in food allergy.
High-resolution DNA copy number and gene expression analyses distinguish chromophobe renal cell carcinomas and renal oncocytomas
Authors: Yusenko Maria V , Kuiper Roland P , Boethe Tamas , Ljungberg Börje , van Kessel Ad Geurts , Kovacs Gyula 
Published: May 2009

Abstract

Background
The diagnosis of benign renal oncocytomas (RO) and chromophobe renal cell carcinomas (RCC) based on their morphology remains uncertain in several cases.

Methods
We have applied Affymetrix GeneChip Mapping 250 K NspI high-density oligoarrays to identify small genomic alterations, which may occur beyond the specific losses of entire chromosomes, and also Affymetrix GeneChip HG-U133 Plus2.0 oligoarrays for gene expression profiling.

Results
By analysing of DNA extracted from 30 chRCCs and 42 ROs, we have confirmed the high specificity of monosomies of chromosomes 1, 2, 6, 10, 13, 17 and 21 in 70–93% of the chRCCs, while ROs displayed loss of chromosome 1 and 14 in 24% and 5% of the cases, respectively. We demonstrated that chromosomal gene expression biases might correlate with chromosomal abnormalities found in chromophobe RCCs and ROs. The vast majority genes downregulated in chromophobe RCC were mapped to chromosomes 2, 6, 10, 13 and 17. However, most of the genes overexpressed in chromophobe RCCs were located to chromosomes without any copy number changes indicating a transcriptional regulation as a main event.

Conclusion
The SNP-array analysis failed to detect recurrent small deletions, which may mark loci of genes involved in the tumor development. However, we have identified loss of chromosome 2, 10, 13, 17 and 21 as discriminating alteration between chromophobe RCCs and ROs. Therefore, detection of these chromosomal changes can be used for the accurate diagnosis in routine histology.
A typhoid fever outbreak in a slum of South Dumdum municipality, West Bengal, India, 2007: Evidence for foodborne and waterborne transmission
Authors: Bhunia Rama , Hutin Yvan , Ramakrishnan Ramachandran , Pal Nishith , Sen Tapas , Murhekar Manoj 
Published: May 2009

Abstract

Background
In April 2007, a slum of South Dumdum municipality, West Bengal reported an increase in fever cases. We investigated to identify the agent, the source and to propose recommendations.

Methods
We defined a suspected case of typhoid fever as occurrence of fever for ≥ one week among residents of ward 1 of South Dumdum during February – May 2007. We searched for suspected cases in health care facilities and collected blood specimens. We described the outbreak by time, place and person. We compared probable cases (Widal positive >= 1:80) with neighbourhood-matched controls. We assessed the environment and collected water specimens.

Results
We identified 103 suspected cases (Attack rate: 74/10,000, highest among 5–14 years old group, no deaths). Salmonella (enterica) Typhi was isolated from one of four blood specimens and 65 of 103 sera were >= 1:80 Widal positive. The outbreak started on 13 February, peaked twice during the last week of March and second week of April and lasted till 27 April. Suspected cases clustered around three public taps. Among 65 probable cases and 65 controls, eating milk products from a sweet shop (Matched odds ratio [MOR]: 6.2, 95% confidence interval [CI]: 2.4–16, population attributable fraction [PAF]: 53%) and drinking piped water (MOR: 7.3, 95% CI: 2.5–21, PAF-52%) were associated with illness. The sweet shop food handler suffered from typhoid in January. The pipelines of intermittent non-chlorinated water supply ran next to an open drain connected with sewerage system and water specimens showed faecal contamination.

Conclusion
The investigation suggested that an initial foodborne outbreak of typhoid led to the contamination of the water supply resulting in a secondary, waterborne wave. We educated the food handler, repaired the pipelines and ensured chlorination of the water.
Improving protein structure similarity searches using domain boundaries based on conserved sequence information
Authors: Thompson Kenneth Evan , Wang Yanli , Madej Tom , Bryant Stephen H 
Published: May 2009

Abstract

Background
The identification of protein domains plays an important role in protein structure comparison. Domain query size and composition are critical to structure similarity search algorithms such as the Vector Alignment Search Tool (VAST), the method employed for computing related protein structures in NCBI Entrez system. Currently, domains identified on the basis of structural compactness are used for VAST computations. In this study, we have investigated how alternative definitions of domains derived from conserved sequence alignments in the Conserved Domain Database (CDD) would affect the domain comparisons and structure similarity search performance of VAST.

Results
Alternative domains, which have significantly different secondary structure composition from those based on structurally compact units, were identified based on the alignment footprints of curated protein sequence domain families. Our analysis indicates that domain boundaries disagree on roughly 8% of protein chains in the medium redundancy subset of the Molecular Modeling Database (MMDB). These conflicting sequence based domain boundaries perform slightly better than structure domains in structure similarity searches, and there are interesting cases when structure similarity search performance is markedly improved.

Conclusion
Structure similarity searches using domain boundaries based on conserved sequence information can provide an additional method for investigators to identify interesting similarities between proteins with known structures. Because of the improvement in performance of structure similarity searches using sequence domain boundaries, we are in the process of implementing their inclusion into the VAST search and MMDB resources in the NCBI Entrez system.
Validity and reliability of the Child Perceptions Questionnaires applied in Brazilian children
Authors: Barbosa Taís S , Tureli Maria Claudia M , Gavião Maria Beatriz D 
Published: May 2009

Abstract

Background
The Child Perceptions Questionnaires (CPQ8–10 and CPQ11–14) are indicators of child oral health-related quality of life. The aim of this study was to assess the validity and reliability of the self-applied CPQ8–10 and CPQ11–14 in Brazilian children, after translations and cultural adaptations in the Brazilian Portuguese language.

Methods
Schoolchildren were recruited from general populations for pre-testing (n = 80), validity (n = 210), and test-retest reliability (n = 50) studies. They were also examined for dental caries, gingivitis, fluorosis, and malocclusion.

Results
Children with greater dental caries experience in primary dentition had higher impacts on CPQ domains. Girls had higher scores for CPQ8–10 domains than boys. Mean CPQ11–14 scores were highest for 11-year-old children and lowest for 14-year-old children. Construct validity was supported by significant associations between the CPQ8–10 and CPQ11–14 scores and the global rating of oral health (r = 0.38, r = 0.43) and overall well-being (r = 0.39, r = 0.60), respectively. The Cronbach's alpha was 0.95 for both questionnaires. The test-retest reliabilities of the overall CPQ8–10 and CPQ11–14 scores were both excellent (ICC = 0.96, ICC = 0.92).

Conclusion
The Brazilian Portuguese version of CPQ8–10 and CPQ11–14 was valuable and reliable for use in the Brazilian child population, although discriminant validity was sporadic due to the fact that impacts are mediated by others factors, such personal, social, and environmental variables.
Studies on the antimicrobial activity and brine shrimp toxicity of Zeyheria tuberculosa (Vell.) Bur. (Bignoniaceae) extracts and their main constituents
Authors: Bastos Maria Lysete A , Lima Maria Raquel F , Conserva Lucia M , Andrade Vânia S , Rocha Eliana MM , Lemos Rosangela PL 
Published: May 2009

Abstract

Background
Due to the indiscriminate use of antimicrobial drugs, the emergence of human pathogenic microorganisms resistant to major classes of antibiotics has been increased and has caused many clinical problems in the treatment of infectious diseases. Thus, the aim of this study was to evaluate for the first time the in vitro antimicrobial activity and brine shrimp lethality of extracts and isolated compounds from Zeyheria tuberculosa (Vell.) Bur., a species used in Brazilian folk medicine for treatment of cancer and skin diseases.

Methods
Using the disc diffusion method, bioautography assay and brine shrimp toxicity test (Artemia salina Leach), we studied the antimicrobial activity and lethality of extracts and isolated compounds against three microorganisms strains, including Gram-positive (Staphylococcus aureus) and Gram-negative (Pseudomonas aeruginosa) bacteria and yeasts (Candida albicans).

Results
In this study, the extracts inhibited S. aureus (8.0 ± 0.0 to 14.0 ± 0.0 mm) and C. albicans (15.3 ± 0.68 to 25.6 ± 0.4 mm) growth. In the brine shrimp test, only two of them showed toxic effects (LC50 29.55 to 398.05 μg/mL) and some extracts were non-toxic or showed weak lethality (LC50 705.02 to > 1000 μg/mL). From these extracts, four flavones [5,6,7,8-tetramethoxyflavone (1), 5,6,7-trimethoxyflavone (2), 4'-hydroxy-5,6,7,8-tetramethoxyflavone (3), and 4'-hydroxy-5,6,7-trimethoxyflavone (4)] were isolated through bioassay-guided fractionation and identified based on the 1D and 2D NMR spectral data. By bioautography assays, compounds 1 [S. aureus (16.0 ± 0.0 mm) and C. albicans (20.0 ± 0.0 mm)] and 3 [S. aureus (10.3 ± 0.6 mm) and C. albicans (19.7 ± 0.6 mm)] inhibited both microorganisms while 2 inhibited only S. aureus (11.7 ± 0.6 mm). Compound 4 did not restrain the growth of any tested microorganism.

Conclusion
Our results showed that extracts and isolated flavones from Z. tuberculosa may be particularly useful against two pathogenic microorganisms, S. aureus and C. albicans. These results may justify the popular use this species since some fractions tested had antimicrobial activity and others showed significant toxic effects on brine shrimps. However, in order to evaluate possible clinical application in therapy of infectious diseases, further studies about the safety and toxicity of isolated compounds are needed.
Identifying candidate sites for crop biofortification in Latin America: case studies in Colombia, Nicaragua and Bolivia
Authors: Zapata-Caldas Emmanuel , Hyman Glenn , Pachón Helena , Monserrate Fredy Alexander , Varela Liliana Vesga 
Published: May 2009

Abstract

Background
Agricultural science can address a population's vitamin, amino acid and mineral malnutrition through biofortification - agronomy, plant breeding and biotechnology to develop crops with high nutrient contents. Biofortified crop varieties should be grown in areas with populations at risk of nutrient deficiency and in areas where the same crop is already grown and consumed. Information on the population at risk of nutrient deficiency is rarely available for sub-national administrative units, such as provinces, districts, and municipalities. Nor is this type of information commonly analyzed with data on agricultural production. This project developed a method to identify populations at risk of nutrient deficiency in zones with high crop production, places where biofortification interventions could be targeted.

Results
Nutrient deficiency risk data were combined with crop production and socioeconomic data to assess the suitability of establishing an intervention. Our analysis developed maps of candidate sites for biofortification interventions for nine countries in Latin America and the Caribbean. Results for Colombia, Nicaragua, and Bolivia are presented in this paper. Interventions in northern Colombia appear promising for all crops, while sites for bean biofortification are widely scattered throughout the country. The most promising sites in Nicaragua are found in the center-north region. Candidate sites for biofortification in Bolivia are found in the central part of the country, in the Andes Mountains. The availability and resolution of data limits the analysis. Some areas show opportunities for biofortification of several crops, taking advantage of their spatial coincidence. Results from this analysis should be confirmed by experts or through field visits.

Conclusion
This study demonstrates a method for identifying candidate sites for biofortification interventions. The method evaluates populations at risk of nutrient deficiencies for sub-national administrative regions, and provides a reasonable alternative to more costly, information-intensive approaches.
Src, PKCα, and PKCδ are required for αvβ3 integrin-mediated metastatic melanoma invasion
Authors: Putnam Andrew J , Schulz Veronique V , Freiter Eric M , Bill Heather M , Miranti Cindy K 
Published: May 2009

Abstract

Background
Integrins, cell-surface receptors that mediate adhesive interactions between cells and the extracellular matrix (ECM), play an important role in cancer progression. Expression of the vitronectin receptor αvβ3 integrin correlates with increased invasive and metastatic capacity of malignant melanomas, yet it remains unclear how expression of this integrin triggers melanoma invasion and metastasis.

Results
Two melanoma cell lines C8161.9 and M14 both express high levels of αvβ3 integrin and adhere to vitronectin. However, only the highly metastatic C8161.9 cells are capable of invading vitronectin-enriched Matrigel in an αvβ3-depenent manner. Elevated levels of PKCα and PKCδ, and activated Src were detected specifically in the highly metastatic melanoma cells, but not in the low metastatic M14 cells. Inhibition of Src or PKC activity suppressed αvβ3-dependent invasion. Furthermore, over expression of Src or PKCα and PKCδ was sufficient to confer αvβ3-dependent invasiveness to M14 cells. Stress fiber formation and focal adhesion formation were almost completely absent in C8161.9 cells compared to M14 cells. Inhibition of Src signaling was sufficient to restore normal actin architecture, and resulted in decreased p190RhoGAP phosphorylation and enhanced RhoA activity. Src had no effect on Rac activity. Loss of PKCα expression, but not PKCδ, by siRNA inhibited Rac and PAK activity as well as invasiveness. Loss of PKCα restored focal adhesion formation and partially restored stress fiber formation, while loss of PKCδ primarily restored stress fibers.

Conclusion
The misregulated expression of PKCα and PKCδ and elevated Src activity in metastatic melanoma cells is required for efficient αvβ3-mediated invasion. PKCα and Src enhance αvβ3-mediated invasion in part by increasing the GTPase activity of Rac relative to RhoA. PKCα influences focal adhesion formation, while PKCδ controls stress fibers.
An approach to evaluate the topological significance of motifs and other patterns in regulatory networks
Authors: Goemann Björn , Wingender Edgar , Potapov Anatolij P 
Published: May 2009

Abstract

Background
The identification of network motifs as statistically over-represented topological patterns has become one of the most promising topics in the analysis of complex networks. The main focus is commonly made on how they operate by means of their internal organization. Yet, their contribution to a network's global architecture is poorly understood. However, this requires switching from the abstract view of a topological pattern to the level of its instances. Here, we show how a recently proposed metric, the pairwise disconnectivity index, can be adapted to survey if and which kind of topological patterns and their instances are most important for sustaining the connectivity within a network.

Results
The pairwise disconnectivity index of a pattern instance quantifies the dependency of the pairwise connections between vertices in a network on the presence of this pattern instance. Thereby, it particularly considers how the coherence between the unique constituents of a pattern instance relates to the rest of a network. We have applied the method exemplarily to the analysis of 3-vertex topological pattern instances in the transcription networks of a bacteria (E. coli), a unicellular eukaryote (S. cerevisiae) and higher eukaryotes (human, mouse, rat). We found that in these networks only very few pattern instances break lots of the pairwise connections between vertices upon the removal of an instance. Among them network motifs do not prevail. Rather, those patterns that are shared by the three networks exhibit a conspicuously enhanced pairwise disconnectivity index. Additionally, these are often located in close vicinity to each other or are even overlapping, since only a small number of genes are repeatedly present in most of them. Moreover, evidence has gathered that the importance of these pattern instances is due to synergistic rather than merely additive effects between their constituents.

Conclusion
A new method has been proposed that enables to evaluate the topological significance of various connected patterns in a regulatory network. Applying this method onto transcriptional networks of three largely distinct organisms we could prove that it is highly suitable to identify most important pattern instances, but that neither motifs nor any pattern in general appear to play a particularly important role per se. From the results obtained so far, we conclude that the pairwise disconnectivity index will most likely prove useful as well in identifying other (higher-order) pattern instances in transcriptional and other networks.
Bioprospecting metagenomes: glycosyl hydrolases for converting biomass
Authors: Li Luen-Luen , McCorkle Sean R , Monchy Sebastien , Taghavi Safiyh , van der Lelie Daniel 
Published: May 2009

Abstract
Throughout immeasurable time, microorganisms evolved and accumulated remarkable physiological and functional heterogeneity, and now constitute the major reserve for genetic diversity on earth. Using metagenomics, namely genetic material recovered directly from environmental samples, this biogenetic diversification can be accessed without the need to cultivate cells. Accordingly, microbial communities and their metagenomes, isolated from biotopes with high turnover rates of recalcitrant biomass, such as lignocellulosic plant cell walls, have become a major resource for bioprospecting; furthermore, this material is a major asset in the search for new biocatalytics (enzymes) for various industrial processes, including the production of biofuels from plant feedstocks. However, despite the contributions from metagenomics technologies consequent upon the discovery of novel enzymes, this relatively new enterprise requires major improvements. In this review, we compare function-based metagenome screening and sequence-based metagenome data mining, discussing the advantages and limitations of both methods. We also describe the unusual enzymes discovered via metagenomics approaches, and discuss the future prospects for metagenome technologies.