bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simulating STEM Imaging of Nanoparticles in Micrometers-Thick Substrates
Authors: Demers H. , Poirier-Demers N. , Drouin D. , de Jonge N. 
Published: October 2010

AbstractScanning transmission electron microscope (STEM) images of three-dimensional (3D) samples were simulated. The samples consisted of a micrometer(s)-thick substrate and gold nanoparticles at various vertical positions. The atomic number (Z) contrast as obtained via the annular dark-field detector was generated. The simulations were carried out using the Monte Carlo method in the CASINO software (freeware). The software was adapted to include the STEM imaging modality, including the noise characteristics of the electron source, the conical shape of the beam, and 3D scanning. Simulated STEM images of nanoparticles on a carbon substrate revealed the influence of the electron dose on the visibility of the nanoparticles. The 3D datasets obtained by simulating focal series showed the effect of beam broadening on the spatial resolution and on the signal-to-noise ratio. Monte Carlo simulations of STEM imaging of nanoparticles on a thick water layer were compared with experimental data by programming the exact sample geometry. The simulated image corresponded to the experimental image, and the signal-to-noise levels were similar. The Monte Carlo simulation strategy described here can be used to calculate STEM images of objects of an arbitrary geometry and amorphous sample composition. This information can then be used, for example, to optimize the microscope settings for imaging sessions where a low electron dose is crucial for the design of equipment, or for the analysis of the composition of a certain specimen.
Expression of adhesion molecules on cord‐blood‐derived, cultured human mast cells and effect of dexamethasone on intercellular adhesion molecule‐1 expression on the mast cells treated by phorbol myristate acetate
Authors: Inamura H. , Kurosawa M. , Kuwasaki T. , Kamada Y. , Kayaba H. , Chihara J. 
Published: October 2010

Background: Increase in mast‐cell number at sites of allergic inflammation has been observed, and glucocorticoids applied to the sites have been shown to result in a significant reduction in mast cells. However, the expression of adhesion molecules on cultured human mast cells and their regulation by glucocorticoids is poorly understood. Methods: Cultured human mast cells were raised from human umbilical cord‐blood cells, and the expression of adhesion molecules on the mast cells was analyzed by flow cytometry. The cells were also incubated with 10 ng/ml phorbol myristate acetate (PMA) for the indicated time, and the effect of dexamethasone on adhesion molecule expression on PMA‐treated, cultured human mast cells was examined. Results: Cord‐blood‐derived, cultured human mast cells constitutively expressed intercellular adhesion molecule‐1 (ICAM‐1), very late antigen‐4 (VLA‐4), and macrophage‐1 antigen (Mac‐1). Weak expression of lymphocyte function‐associated antigen‐1 (LFA‐1) was observed on the cells, whereas they failed to express vascular cell adhesion molecule‐1 (VCAM‐1). Kinetic studies showed that after a transient downregulation reaching a minimum at 8 h, the expression of ICAM‐1 was markedly upregulated on PMA‐treated mast cells after a 24‐h incubation. In contrast, the expression of VLA‐4 and Mac‐1 was decreased after the incubation with PMA for 24 h. The PMA‐induced upregulation of ICAM‐1 was inhibited by dexamethasone in a concentration‐dependent manner. Conclusions: Our results indicate that cord‐blood‐derived, cultured human mast cells constitutively express integrins and ICAM‐1, but not VCAM‐1, and demonstrate for the first time that dexamethasone inhibits the upregulation of ICAM‐1 on PMA‐treated, cultured human mast cells.
Gas phase bond dissociation enthalpies and enthalpies of isomerization/reaction for small hydrocarbon combustion related compounds between 300 and 1500 K: A comparison of Gaussian-4 (G4) theoretical values against experimental data
Authors: Rayne Sierra , Forest Kaya 
Published: October 2010

AbstractGas phase calculations at 1 atmosphere pressure between 300 and 1500 K at 200 K intervals were conducted using the Gaussian-4 (G4) composite method level of theory on a representative set of reactions having broad relevance in hydrocarbon combustion chemistry. Reasonable agreement between the experimental and theoretical data was obtained across the temperature range under consideration for all bond dissociation enthalpies, isomerization enthalpies, and enthalpies of reaction. For some reaction schemes, chemical accuracy for the theoretical method was maintained over the complete temperature range, whereas other systems displayed up to several kcal mol^-1^ deviations from experimental data. The direction of signed errors generally increased as the temperature was raised, and no general error trends were related to molecular size or reaction class.
Reactome: A database of biological pathways
Authors: Croft David 
Published: October 2010

AbstractREACTOME is an open-source, open access, manually curated, peer-reviewed and highly reliable pathway database. A new website is currently in preparation, which includes tools for visualising pathway diagrams and analyzing user-supplied data in a pathway context. Reactome provides facilities for exporting its content in BioPax and SBML formats.
Omics Data Sharing - BioSharing: on Data Policies’s Plans and Reporting Standards
Authors: Sansone Susanna-Assunta 
Published: October 2010

AbstractSeveral data preservation, management and sharing policies have emerged in response to increased funding for high-throughput approaches in major genomics and functional genomics bioscience domain; and nowadays, several funding agencies also require inclusion of data-sharing plans in grant applications. But despite some commonalities, the policies are heterogeneous by nature, given the different types of communities served and the data types they generate. In parallel, an escalating number of community-driven standardization efforts (including biocurators, database developers and experimentalists, vendors etc), operate to develop minimal requirements checklists, ontologies, and file-formats to support the harmonization of the reporting process, so that different experiments and data can be easily shared, compared, and integrated. The proliferation of these standardization efforts is a positive sign of community engagement, but it also brings with it new sociological and technological challenges - creating interoperability and avoiding unnecessary overlaps and duplication of efforts that hampers their wider uptake. Let aside the ethical, commercialization, credit and other known issues arising from public data release, basic communication channels still need to be formally created and maintained, especially between the funders and the standardization efforts to enable flow of information and mutual support. For example, funding agencies should keep abreast of challenges the standardization efforts face so that they can provide targeted funds to sustain their development and maintenance; when standards-compliant systems become available these should be channeled to the appropriate funding agencies that in turn can recommend them in the data sharing policy. Hence the creation of the BioSharing forum on data policies’s plans and reporting standards, stemming from an initial collaboration with a range of representatives from US, UK and European funding agencies (Field D., Sansone SA, et al. (2009), Science, 9, 234-236; "www.biosharing.org":http://www.biosharing.org, "www.isa-tools.org":http://www.isa-tools.org); our dialogue will continue to formalize linkages between funders, implementing data sharing policies, and well-constituted standardization efforts in the biosciences domain and in close collaboration with the Biocuration Society.
Gene Curation Software at the Rat Genome Database (RGD)
Authors: Wang Shur-Jen , Kowalski George , Smith Jennifer , Dwinell Melinda , Nigam Rajni , Munzenmaier Diane , De Pons Jeff , Jacob Howard , Laulederkind Stanley , Shimoyama Mary , Taylor Brad , Petri Victoria , Lowry Timothy , Liu Weisong , Hayman G. Thomas 
Published: October 2010

AbstractAt model organism databases data is curated for numerous biological categories using various ontologies and vocabularies. The Rat Genome Database (RGD) uses four different ontologies to standardize annotation information for genes and their associations with disease, phenotypes, and pathways. For manual gene curation this is all done in a single user interface of a web-based annotation tool developed at RGD. The same interface can be used for the curation of QTLs and strains. The development of the tool has been achieved through a collaboration of curators and software developers. Features have been tailored to the needs of the curators to allow optimum efficiency of the data entry portion of the curation process. Annotations using the Gene Ontology, Mammalian Phenotype Ontology, Pathway Ontology, and Disease Ontology can be done simultaneously in the same user interface. The search function of the tool has multiple options, giving the curators the opportunity to specify the search according to the immediate need. For ontology terms, gene, QTL, and strain objects the tool searches RGD data tables. For references the tool searches both internal and PubMed reference IDs. If an abstract reference is not already found at RGD, the tool automatically downloads the reference and assigns an RGD ID to it. Data objects, ontology terms, and references can be stored in multiples, providing various options for composing annotations. An editing step allows the composed annotation line to be altered before entering it in the database. The tool displays all current annotations for any gene that is selected. A second editing function is available by hyperlink for any pre-existing annotation displayed in the tool. The curation software has more than doubled literature curation production since replacing spreadsheet curation.
Chinese herbal extracts (SK0506) as a potential candidate for the therapy of the metabolic syndrome
Authors: Tan Yi , Kamal Mohammad A. , Wang Zheng-Zhong , Xiao Wei , Seale John P. , Qu Xianqin 
Published: October 2010

The metabolic syndrome has reached epidemic proportions worldwide, but currently there is a lack of effective therapies for this multifactorial endocrine disease. TCM (traditional Chinese medicine) has been utilized to treat a wide variety of diseases for centuries in the People's Republic of China, subsequently becoming a promising source for the development of new therapeutic agents. Chinese medicinal herbs Gynostemma pentaphyllum, Coptis chinensis and Salvia miltiorrhiza have been shown to have anti-atherosclerotic and antidiabetic properties. In this study, we have investigated the metabolic effects of a mixture of these three herbal extracts (SK0506) in a rodent model of the metabolic syndrome induced by an HFD (high-fat diet). SD (Sprague–Dawley) rats that were fed on an HFD for 4 weeks gained 33% more weight compared with chow-fed rats (P&lt;0.05). Four weeks treatment with SK0506 prevented weight gain with decreased visceral fat (P&lt;0.01 compared with vehicle treatment). SK0506 also significantly reduced plasma triacylglycerols (triglycerides), NEFAs (non-esterified fatty acids) and cholesterol. SK0506 exerted similar effects to RSG (rosiglitazone) on impaired glucose intolerance. SK0506 also significantly enhanced glucose uptake and glycogen synthesis in adipose tissue during hyperinsulinaemic–euglycaemic clamp. Western blotting analysis revealed that SK0506 enhanced GLUT4 (glucose transporter 4) expression in adipose tissue, and RSG markedly up-regulated GLUT4 translocation in skeletal muscle. Overall, the present study has discovered that SK0506 can reverse several components of the metabolic syndrome primarily through acting on hyperlipidaemia and visceral obesity. The results from the present study suggest that it is worthwhile to conduct a randomized clinical trial to confirm the potential that SK0506 may be a new oral agent for treating the metabolic syndrome and preventing Type 2 diabetes.
Sensitization to sunflower pollen and lung functions in sunflower processing workers
Authors: Atis S. , Tutluoglu B. , Sahin K. , Yaman M. , Küçükusta A.R. , Oktay I. 
Published: October 2010

Background: This study aimed to investigate whether exposure to sunflower pollen (Helianthus annuus) increases both sensitization and respiratory symptoms, and whether or not it affects lung functions in sunflower processing workers. Methods: The largest sunflower processing factories in the Thrace region of Turkey participated in this study. Workers from the units directly exposed to sunflower seed enrolled as the study group (n = 102) and workers who were not directly exposed to Helianthus annuus pollen (n = 102) were the control group. Detailed questionnaires covering respiratory and allergic symptoms were completed, and skin prick tests and lung function tests were performed. Results: We found a very high rate (23.5%) of sensitization to Helianthus annuus in the study group compared to the controls (P < 0.001). Logistic regression analysis showed that the risk of sensitization to H. annuus was increased 4.7‐fold (odds ratio = 4.17, 95% confidence interval = 1.3–16.7) if subjects were exposed to sunflower pollen in the workplace. While asthmatic symptoms and allergic skin diseases were not different between the two groups, workers in the study group had a higher rate of allergic rhinitis and conjunctivitis (P < 0.05). We found that pulmonary function was significantly impaired in the study group (P < 0.01). Using a multivariate analysis model, inclusion in the study group was found to be a predictive factor for impairment of lung function (P = 0.002). Conclusions: We conclude that sunflower pollen has high allergenic potential, especially when there is close contact, and exposure to sunflower pollen in the workplace can result in impairment in lung function.
Low‐dose local nasal immunotherapy in children with perennial allergic rhinitis due to Dermatophagoides
Authors: Marcucci F. , Sensi L.G. , Caffarelli C. , Cavagni G. , Bernardini R. , Tiri A. , Riva G. , Novembre E. 
Published: October 2010

Background:Allergen specific immunotherapy was known to be useful in the treatment of respiratory allergic disease. Local nasal immunotherapy (LNIT) offers advantages such as a good efficacy/safety ratio and a more convenient allergen delivery. The aim of this study was to assess the safety and clinical efficacy of a modified scheduling of LNIT in 32 children with allergic rhinitis due to Dermatophagoides. Methods:A multicentre, randomized, double‐blind placebo controlled study carried out for two years, with a modified schedule of LNIT treatment: a build‐up phase at increasing dosages from 2.5 AU to 80 AU and a maintenance period at low dosage (80 AU) once a week. Symptom and medication scores, threshold dose with specific nasal provocation test (NPT) and immunological parameters (IgE and IgG4) were evaluated. Results:No important local or systemic side‐effects were observed in children who completed the study. Compared to placebo, the active treatment group showed significant improvement in rhinitis symptoms and a reduction of drug consumption after 18 months of LNIT. These results were confirmed by a significant reduction of allergen specific nasal reactivity. Serum and nasal specific IgE and IgG4 did not show any difference in the two groups. Conclusions:The safety and clinical efficacy of low‐dose LNIT suggests that this therapy may be useful in the treatment of allergic rhinitis disease in children.
A method for applying matrix corrections to X‐ray intensity maps using the Bence–Albee algorithm and Matlab
Authors: Clarke G. L. , Daczko N. R. , Nockolds C. 
Published: October 2010

AbstractMatlab scripts that apply the Bence & Albee (1968) matrix correction algorithm to X‐ray intensity data collected as element maps on a Cameca SX‐50 microprobe are used to produce two‐dimensional maps of oxide weight percent and cation proportions for SiO2, Al2O3, FeO, MnO, MgO, CaO, Na2O and K2O. Once generated, large data sets of mapped oxide weight percent values or cation numbers that retain spatial information can be used petrologically. The technique is used to evaluate the compositional range of barroisitic amphibole in an eclogite from New Caledonia, to examine aspects of equilibration during the partial hydration of the eclogite facies mineral assemblage.
Polyvalent contact allergy to corticosteroids: A report of two cases
Authors: Semrádová V , Dastychová E 
Published: October 2010

AbstractTwo cases of positive allergic reactions to eight patch‐tested corticosteroid substances are reported. The patients were middle‐aged women with a long history of contact dermatitis who had used topical corticosteroids for years. Pure corticosteroid substances were tested in therapeutic and 1% concentrations in ethanol and petrolatum. The intensity of reactions was different depending on the vehicle and concentration. Patients with hypersensitivity to several corticosteroid substances represent an important therapeutic problem.
The circadian and homeostatic modulation of sleep pressure during wakefulness differs between morning and evening chronotypes
Authors: Taillard Jacques , Philip Pierre , Coste Olivier , Sagaspe Patricia , Bioulac Bernard 
Published: October 2010

SummaryThe purpose of this study was to evaluate homeostatic and circadian sleep process in ‘larks’ and ‘owls’ under daily life conditions. Core body temperature, subjective sleepiness and waking electroencephalogram (EEG) theta–alpha activity (6.25–9 Hz) were assessed in 18 healthy men (nine morning and nine evening chronotypes, 21.4 ± 1.9 years) during a 36‐h constant routine that followed a week of a normal ‘working’ sleep–wake schedule (bedtime: 23.30 h, wake time: 07.30 h). The phase of the circadian rhythm of temperature and sleepiness occurred respectively, 1.5 h (P = 0.01) and 2 h (P = 0.009) later in evening‐ than in morning‐type subjects. Only morning‐type subjects showed a bimodal rhythm of sleep–wake propensity. The buildup of subjective sleepiness, as quantified by linear regression, was slower in evening than in morning types (P = 0.04). The time course of EEG theta–alpha activity of both chronotypes could be closely fitted by an exponential curve. The time constant of evening types was longer than that of morning types (P = 0.03), indicating a slower increase in sleep pressure during extended wakefulness. These results suggest that both the circadian signal and the kinetics of sleep pressure buildup differ between the two chronotypes even under prior naturalistic conditions mimicking the usual working day.
Sleep microstructure around sleep onset differentiates major depressive insomnia from primary insomnia
Authors: Staner Luc , Cornette Françoise , Maurice Damien , Viardot Geoffrey , Bon Olivier Le , Haba José , Staner Corinne , Luthringer Rémy , Muzet Alain , Macher Jean‐Paul 
Published: October 2010

SummaryIn the present study we investigate whether alterations of sleep propensity or of wake propensity are implicated in sleep initiation disturbances encountered in major depressive insomnia and in primary insomnia. For this purpose, the time course of electroencephalogram (EEG) power density during the period preceding sleep onset and during the first non‐rapid eye movement (REM) period was examined in three age and gender matched groups of 10 women and 11 men (healthy controls, primary insomniacs and depressive insomniacs). In contrast to healthy controls and depressive insomniacs, patients with primary insomnia did not experience a gradual decrease of their alpha and beta1 power during the sleep onset period and had a lower delta activity in the 5 min preceding sleep onset. Compared with the two other groups, depressive patients exhibit less dynamic changes in slow wave activity during the first non‐REM period. The present results suggest that hyperarousal (high ‘Process W’) may mainly be implicated in the sleep initiation difficulties of primary insomniacs whereas the homeostatic sleep regulation process seems to be partially maintained. In our major depressed patients, the sleep initiation disturbances appeared to relate to a lower sleep pressure (low ‘Process S’) rather than to hyperarousal. This study supports the idea that different mechanisms are implicated in sleep disturbances experienced by primary insomniacs and major depressive insomniacs.
CSF hypocretin measures in patients with obstructive sleep apnea
Authors: Kanbayashi T. , Inoue Y. , Kawanishi K. , Takasaki H. , Aizawa R. , Takahashi K. , Ogawa Y. , Abe M. , Hishikawa Y. , Shimizu T. 
Published: October 2010

SummaryThe majority of patients with narcolepsy‐cataplexy were reported to have very low cerebrospinal fluid (CSF) hypocretin‐1 (orexin‐A) levels. The hypocretin‐1 levels of secondary excessive daytime sleepiness (EDS) disorders are not known. In this study, we found that CSF hypocretin levels in the patients with obstructive sleep apnea syndrome were within the control range. The low hypocretin levels seem to reflect only the presence of cataplexy and DR2 positive in narcoleptics but not EDS itself.
Immunogenicity and safety of two schedules of Hepatitis B vaccination during pregnancy
Authors: Gupta Indu , Ratho Radha K. 
Published: October 2010

AbstractAim:  To test the immunogenicity and safety of Hepatitis B (HB) vaccination during pregnancy and passive transfer of antibodies to the newborn.Methods:  Ninety‐nine HBsAg‐negative pregnant women were divided randomly in two groups; group I was given two, and group II was given three doses of recombinant Hepatitis B vaccine and followed up until 4 months after delivery.Results:  The vaccination was safe. The maternal anti‐HB antibody levels at delivery were significantly higher in three dose schedule as compared to two dose schedule. Similarly, the antibody levels in the newborns were higher in the three dose schedule. The maternal antibody levels were higher at 2 and 4 months post‐delivery in group II but were observed to be declining in the newborns.Conclusion:  Hepatitis B vaccination during pregnancy is safe and highly immunogenic, and there is passive transfer of antibodies to the newborns.
First‐time mothers – identifying their needs, perceptions and experiences
Authors: Cronin Camille 
Published: October 2010

Summary• The aim of this research was to identify needs, perceptions and experiences of first‐time mothers in the postnatal period.• Data were collected through focus groups and in‐depth interviews from a sample of 13 women, 61% were aged 20 years or less, from an urban city area in Southern Ireland. Through content analysis, key themes were identified relating to birth and hospitalization, support, motherhood and psychological issues.• Attendance at antenatal classes was variable and perceptions of being unprepared for birth and motherhood prevailed. Participants appeared shocked at the amount of pain experienced during birth and had little rest during hospitalization. They received physical and emotional support and preparation for childcare from midwives. Breastfeeding, while promoted, by midwives was not acceptable.• The ‘maternal mother’ was key in providing direct childcare, advice and emotional help, support for attendance at school and ‘time out’ to socialize. Support was reciprocal if the maternal mother had young children.• Professional support by public health nurses was well‐established. However, emphasis was perceived to be on ‘baby's development'.• Maternal depression, loneliness, living in homes with limited space and difficulty in ‘letting go’ of baby care to return to school or work were reported.• Implications for antenatal preparation, national policies, motherhood, and the need for further research are discussed.