bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preparation of Simian Foamy Virus Type-1 Vectors
Authors: Park Jeonghae , Mergia Ayalew 
Published: August 2011

INTRODUCTIONFoamy viruses (FVs) are nonpathogenic retroviruses that offer opportunities for efficient and safe gene transfer in various cell types from different species. These viruses have unique replication mechanisms that are distinct from other retroviruses, which may give an advantage to FV-mediated gene transfer. This protocol describes a method for simian foamy virus type-1 (SFV-1) vector preparation and concentration. A transient transfection of vector and packaging constructs allows generation of the SFV-1 vector with titers of 107/mL. The vectors can be further concentrated by 100–200-fold without significant loss of vector titer.
Immunostaining of Mitotic Chromosomes from Drosophila Larval Brain: Figure 1.
Authors: Pimpinelli Sergio , Bonaccorsi Silvia , Fanti Laura , Gatti Maurizio 
Published: August 2011

INTRODUCTIONGood mitotic chromosome preparations are essential for the immunolocalization of chromosomal proteins. Although methanol/acetic acid fixation techniques preserve chromosome morphology very well, they remove a substantial fraction of chromosomal proteins. We have developed fixation/immunostaining procedures, described here, that are suitable for the immunolocalization of proteinaceous components of metaphase chromosomes from larval Drosophila brain cells. These procedures result in good chromosomal quality with minimal removal of proteins.
Mounting Caenorhabditis elegans Embryos for Live Imaging of Embryogenesis: Figure 1.
Authors: Bao Zhirong , Murray John I. 
Published: August 2011

INTRODUCTIONCaenorhabditis elegans has been a key model organism for biomedical research. Light microscopy has played a central role in C. elegans biology. C. elegans is transparent throughout its life cycle, and its physical size, from 50 µm (embryos) to 1 mm (adults), is well suited for light microscopy. Furthermore, it has an invariant body plan that arises from an invariant cell lineage. A wide range of biological processes, from patterns of gene expression to cell migration to neuronal activity, can be readily observed in single cells with a well-defined developmental context. This protocol describes how to collect and mount young C. elegans embryos for live imaging throughout embryogenesis.
Dissection of Third-Instar Drosophila Larvae for Electrophysiological Recording from Neurons
Authors: Marley Richard , Baines Richard A. 
Published: August 2011

INTRODUCTIONThe fruit fly Drosophila melanogaster has been instrumental in expanding our understanding of early aspects of neural development. The use of this model system has greatly added to our knowledge of neural cell-fate determination, axon guidance, and synapse formation. It has also become possible to access and make electrophysiological recordings directly from neurons in situ in an intact central nervous system (CNS), which has facilitated studies of the development and regulation of neuronal signaling. It is possible to obtain electrophysiological recordings from all stages of Drosophila. Exposure of the intact Drosophila CNS is a prerequisite for such electrophysiological recordings. The dissection procedure described here is suitable for third-instar larvae. The dissection should take ∼5 min to complete if all preparation work has been completed in advance. Owing to the short life span of the dissected larva, it is not recommended that the procedure be stopped or the preparation stored for later use.
Whole-Cell Patch Recording from Drosophila Larval Neurons
Authors: Marley Richard , Baines Richard A. 
Published: August 2011

INTRODUCTIONThe fruit fly Drosophila melanogaster has been instrumental in expanding our understanding of early aspects of neural development. The use of this model system has greatly added to our knowledge of neural cell-fate determination, axon guidance, and synapse formation. It has also become possible to access and make electrophysiological recordings directly from neurons in situ in an intact central nervous system (CNS), which has facilitated studies of the development and regulation of neuronal signaling. This protocol describes a procedure for revealing larval motor neurons and applying whole-cell patch recording techniques to these cells. The useful lifetime of first-instar larval preparations is ∼30 min, and that of third-instar CNS preparations is up to 1 h. It is therefore recommended that fresh preparations are used and that no breaks are taken during the procedure, although there may be time to pull and polish a patch pipette.
Soybean Homologs of MPK4 Negatively Regulate Defense Responses and Positively Regulate Growth and Development
Authors: Liu Jian-Zhong , Horstman Heidi D. , Braun Edward , Graham Michelle A. , Zhang Chunquan , Navarre Duroy , Qiu Wen-Li , Lee Yeunsook , Nettleton Dan , Hill John H. , Whitham Steven A. 
Published: August 2011

Abstract
Mitogen-activated protein kinase (MAPK) cascades play important roles in disease resistance in model plant species such as Arabidopsis (Arabidopsis thaliana) and tobacco (Nicotiana tabacum). However, the importance of MAPK signaling pathways in the disease resistance of crops is still largely uninvestigated. To better understand the role of MAPK signaling pathways in disease resistance in soybean (Glycine max), 13, nine, and 10 genes encoding distinct MAPKs, MAPKKs, and MAPKKKs, respectively, were silenced using virus-induced gene silencing mediated by Bean pod mottle virus. Among the plants silenced for various MAPKs, MAPKKs, and MAPKKKs, those in which GmMAPK4 homologs (GmMPK4s) were silenced displayed strong phenotypes including stunted stature and spontaneous cell death on the leaves and stems, the characteristic hallmarks of activated defense responses. Microarray analysis showed that genes involved in defense responses, such as those in salicylic acid (SA) signaling pathways, were significantly up-regulated in GmMPK4-silenced plants, whereas genes involved in growth and development, such as those in auxin signaling pathways and in cell cycle and proliferation, were significantly down-regulated. As expected, SA and hydrogen peroxide accumulation was significantly increased in GmMPK4-silenced plants. Accordingly, GmMPK4-silenced plants were more resistant to downy mildew and Soybean mosaic virus compared with vector control plants. Using bimolecular fluorescence complementation analysis and in vitro kinase assays, we determined that GmMKK1 and GmMKK2 might function upstream of GmMPK4. Taken together, our results indicate that GmMPK4s negatively regulate SA accumulation and defense response but positively regulate plant growth and development, and their functions are conserved across plant species.
Cost‐effectiveness of tobacco control policies in Vietnam: the case of personal smoking cessation support
Authors: Higashi Hideki , Barendregt Jan J. 
Published: August 2011

ABSTRACTAims  To examine the cost‐effectiveness of personal smoking cessation support in Vietnam.Design, setting and participants  We followed‐up the population aged 15 years and over in 2006 to model the costs and health gains associated with five interventions: physician brief advice; nicotine replacement therapy (patch and gum); bupropion; and varenicline. Threshold analysis was undertaken to determine the price levels of pharmaceuticals for the interventions to be cost‐effective. A multi‐state life table model was constructed such that the interventions affect the smoking cessation behaviour of the age cohorts, and the resulting smoking prevalence defines their health outcomes. A health‐care perspective was employed.Measurements  Cost‐effectiveness is measured in 2006 Vietnamese Dong (VND) per disability‐adjusted life year (DALY) averted. We adopted the World Health Organization thresholds of being ‘cost‐effective’ if less than three times gross domestic product (GDP) per capita (VND 34 600 000) and ‘very cost‐effective’ if less than GDP per capita (VND 11 500 000).Findings  The cost‐effectiveness result of physician brief advice was VND 1 742 000 per DALY averted (international dollars 543), which was ‘very cost‐effective’. Varenicline dominated bupropion and nicotine‐replacement therapies, although it did not fall within the range of being ‘cost‐effective’ under different scenarios. The threshold analysis revealed that prices of pharmaceuticals must be substantially lower than the levels from other countries if pharmacological therapies are to be cost‐effective in Vietnam.Conclusions  Physician brief advice is a cost‐effective intervention and should be included in the priority list of tobacco control policy in Vietnam. Pharmacological therapies are not cost‐effective, and so they are not recommended in Vietnam at this time unless pharmaceuticals could be produced locally at substantially lower costs in the future.
Rhinitis symptoms caused by grass pollen are associated with elevated basophile allergen sensitivity and a larger grass‐specific immunoglobulin E fraction
Authors: Zidarn M. , Košnik M. , Šilar M. , Grahek A. , Korošec P. 
Published: August 2011

SummaryBackgroundThe mechanisms responsible for the difference between clinically irrelevant IgE‐sensitization and allergic rhinitis are not fully understood.ObjectiveWe evaluated the humoral and cellular mechanisms that may be associated with the presence of allergic rhinitis symptoms.MethodsWe selected 26 subjects with positive grass pollen skin tests and IgE antibodies to Timothy (g6) and the major grass allergens rPhl p 1, 5b. Fourteen of those patients reported a history of allergic rhinitis. During winter, we performed a grass pollen CD63 basophile activation test using four log allergen concentrations, followed by a grass nasal provocation test (NPT). We obtained symptom scores in the subsequent pollination season.ResultsWe showed that subjects with a positive NPT have significantly higher CD63 basophile grass pollen responsiveness than NPT‐negative subjects, preferably at submaximal allergen concentrations, which represent cellular sensitivity. Moreover, basophile sensitivity positively correlated with the size of the grass‐specific IgE fraction in relation to total IgE, and it was highly predictive of allergic rhinitis symptoms in the following pollination season.Conclusion and Clinical RelevanceAllergic rhinitis symptoms are significantly associated with allergen‐specific basophile sensitivity. In vitro evaluation of basophile sensitivity should prove useful for distinguishing clinical phenotype of allergic sensitization.
Histological and molecular features of lipomatous and nonlipomatous adipose tissue in familial partial lipodystrophy caused by LMNA mutations
Authors: Araújo‐Vilar D. , Victoria B. , González‐Méndez B. , Barreiro F. , Fernández‐Rodríguez B. , Cereijo R. , Gallego‐Escuredo J.M. , Villarroya F. , Pañeda‐Menéndez A. 
Published: August 2011

SummaryObjectives  Type 2 familial partial lipodystrophy (FPLD2) is a rare adipose tissue (AT) disease caused by mutations in LMNA, in which lipomas appear occasionally. In this study, we aimed to histologically characterize FPLD2‐associated lipomatosis and study the expression of genes and proteins involved in cell cycle control, mitochondrial function, inflammation and adipogenesis.Design and patients  One lipoma and perilipoma fat from each of four subjects with FPLD2 and 10 control subjects were analysed by optical microscopy. The presence of inflammatory cells was evaluated by immunohistochemistry. Real‐time RT‐PCR and Western blot were used to evaluate gene and protein levels.Results  Adipocytes from lipodystrophic patients were significantly larger than those of controls, in both the lipomas and perilipoma fat. Lipodystrophic AT exhibited CD68+ macrophages and CD3+ lymphocytes infiltration. TP53 expression was reduced in all types of lipomas. At protein level, C/EBPβ, p53 and pRb were severely disturbed in both lipodystrophic lipomas and perilipoma fat coming from lipoatrophic areas, whereas the expression of CEBPα was normal. Mitochondrial function genes were less expressed in lipoatrophic fat. In both lipomas and perilipoma fat from lipoatrophic areas, the expression of adipogenes was lower than controls.Conclusions  Even in lipomas, the adipogenic machinery is impaired in lipodystrophic fat coming from lipoatrophic regions in FPLD2, although the histological phenotype is near‐normal, exhibiting low‐grade inflammatory features. Our results suggest that the p53 pathway and some adipogenic proteins, such as CEBPα, could contribute to the maintenance of this near normal phenotype in the remnant AT present in these patients.
Functional and structural evaluation of hearing in acromegaly
Authors: Aydin Kadriye , Ozturk Burak , Turkyilmaz Meral Didem , Dagdelen Selcuk , Ozgen Burce , Unal Faruk , Erbas Tomris 
Published: August 2011

SummaryContext  The impact of acromegaly on the auditory system remains unknown.Objective  This study aimed to examine audiological symptoms and the structure and function of the auditory system in patients with acromegaly.Design/Setting and Patients  The study included 44 patients with acromegaly. Pure tone audiometry, speech audiometry, tympanometry, otoacoustic emissions testing, computerized tomography of the temporal bone and magnetic resonance imaging of the ear were performed in all patients. The study also included 36 age‐ and sex‐matched healthy controls. The patients with acromegaly were divided into three subgroups, as follows: controlled disease (n = 13); partially controlled disease (n = 16); uncontrolled disease (n = 15).Results  In all, 43% of the patients with acromegaly had hearing loss, and 20% had had an episode of otitis in at least one ear. Median pure tone average (PTA) in the patients with acromegaly was 12.5 dB (range: 2–72 dB), vs 8.3 dB (range: 0–20 dB) in the control group (P < 0.001). PTA did not differ significantly between the three patient subgroups. Audiometric tests showed various degrees of hearing loss in at least one ear in 21 patients (48%). Conductive, sensorineural and mixed type hearing loss in at least one ear was noted in 9%, 30% and 18% of the patients, respectively. Auditory imaging showed that 50% of the patients had temporomandibular joint degeneration (TMJD).Conclusions  Hearing loss is quite common in patients with acromegaly. Contrary to common belief, in this study, conductive hearing loss did not occur more frequently than other types. Based on PTA findings in the controls and patients with acromegaly, acromegaly caused hearing loss, but the level of disease activity had no effect on hearing. Middle ear pressure problems might be caused by increased perilymph because of growth hormone (GH)‐related volume overload.
Coral reefs modify their seawater carbon chemistry – case study from a barrier reef (Moorea, French Polynesia)
Authors: Kleypas Joan A. , Anthony Kenneth R. N. , Gattuso Jean‐Pierre 
Published: August 2011

AbstractChanges in the carbonate chemistry of coral reef waters are driven by carbon fluxes from two sources: concentrations of CO2 in the atmospheric and source water, and the primary production/respiration and calcification/dissolution of the benthic community. Recent model analyses have shown that, depending on the composition of the reef community, the air‐sea flux of CO2 driven by benthic community processes can exceed that due to increases in atmospheric CO2 (ocean acidification). We field test this model and examine the role of three key members of benthic reef communities in modifying the chemistry of the ocean source water: corals, macroalgae, and sand. Building on data from previous carbon flux studies along a reef‐flat transect in Moorea (French Polynesia), we illustrate that the drawdown of total dissolved inorganic carbon (CT) due to photosynthesis and calcification of reef communities can exceed the draw down of total alkalinity (AT) due to calcification of corals and calcifying algae, leading to a net increase in aragonite saturation state (Ωa). We use the model to test how changes in atmospheric CO2 forcing and benthic community structure affect the overall calcification rates on the reef flat. Results show that between the preindustrial period and 1992, ocean acidification caused reef flat calcification rates to decline by an estimated 15%, but loss of coral cover caused calcification rates to decline by at least three times that amount. The results also show that the upstream–downstream patterns of carbonate chemistry were affected by the spatial patterns of benthic community structure. Changes in the ratio of photosynthesis to calcification can thus partially compensate for ocean acidification, at least on shallow reef flats. With no change in benthic community structure, however, ocean acidification depressed net calcification of the reef flat consistent with findings of previous studies.
Quantitative approaches in climate change ecology
Authors: Brown Christopher J. , Schoeman David S. , Sydeman William J. , Brander Keith , Buckley Lauren B. , Burrows Michael , Duarte Carlos M. , Moore Pippa J. , Pandolfi John M. , Poloczanska Elvira , Venables William , Richardson Anthony J. 
Published: August 2011

AbstractContemporary impacts of anthropogenic climate change on ecosystems are increasingly being recognized. Documenting the extent of these impacts requires quantitative tools for analyses of ecological observations to distinguish climate impacts in noisy data and to understand interactions between climate variability and other drivers of change. To assist the development of reliable statistical approaches, we review the marine climate change literature and provide suggestions for quantitative approaches in climate change ecology. We compiled 267 peer‐reviewed articles that examined relationships between climate change and marine ecological variables. Of the articles with time series data (n = 186), 75% used statistics to test for a dependency of ecological variables on climate variables. We identified several common weaknesses in statistical approaches, including marginalizing other important non‐climate drivers of change, ignoring temporal and spatial autocorrelation, averaging across spatial patterns and not reporting key metrics. We provide a list of issues that need to be addressed to make inferences more defensible, including the consideration of (i) data limitations and the comparability of data sets; (ii) alternative mechanisms for change; (iii) appropriate response variables; (iv) a suitable model for the process under study; (v) temporal autocorrelation; (vi) spatial autocorrelation and patterns; and (vii) the reporting of rates of change. While the focus of our review was marine studies, these suggestions are equally applicable to terrestrial studies. Consideration of these suggestions will help advance global knowledge of climate impacts and understanding of the processes driving ecological change.
Could our fisheries be more productive? Indirect negative effects of bottom trawl fisheries on fish condition
Authors: Hiddink Jan G. , Johnson Andrew F. , Kingham Rachel , Hinz Hilmar 
Published: August 2011

Summary1. The nets used in bottom trawl fisheries cause mortality of benthic invertebrates and this can decrease the long‐term availability of prey to exploited fish species by reducing the abundance of benthic invertebrates. This may have consequences for the sustainability of fisheries.2. We assessed the impact of bottom trawling on the food availability of fish by comparing the condition of fish (as weight‐at‐length) in an area that had a steep commercial bottom‐trawling gradient in the Irish Sea but otherwise homogeneous environmental conditions.3. We found that the condition of the important commercial flatfish plaice Pleuronectes platessa was negatively related to trawling frequency, and this could be explained by a reduced production of the infaunal invertebrates they feed on. Density‐dependent changes in competition over food could not explain this difference. No effect of trawling on the condition of the flatfish dab Limanda limanda was detected. Whiting Merlangius merlangus feeds primarily on fish, and therefore, no effect of bottom trawling on its condition was expected or detected.4. This study therefore indicates that bottom trawl fisheries may have a negative effect on the condition of some of their target species, but not others, by reducing the abundance of their benthic prey.5. Synthesis and application. Bottom trawls may indirectly affect the population size and growth rate of the target fish species and result in lower fishing yields. Such reductions in the yield and sustainability of fisheries are highly undesirable. The effects of bottom trawls may be mitigated by the modification of fishing gears or by minimizing the area of the seabed fished by bottom trawls.
Observation of health technologies after their introduction into clinical practice: a systematic review on data collection instruments
Authors: Varela‐Lema Leonor , Ruano‐Ravina Alberto , Cerdá Mota Teresa 
Published: August 2011

AbstractRationale, aims and objectives  Early assessment of health technologies after they are covered by the health system is deemed crucial to promptly identify and analyse unforeseen problems that may arise when these are used in real world settings. This paper aims to describe the various instruments which could be used for collecting information intended for prospective observation of health technologies, so as to choose the specific instrument best suited to each context.Methods  Systematic review of the medical literature aimed at retrieving general reference documents on data collection instruments for post‐introduction observation of health technologies. A purpose‐designed systematic bibliographic search was elaborated for the main three data collection instruments identified.Results  The three instruments are briefly described along with the main results of the studies retrieved, in terms of the advantages, drawbacks and considerations to be borne in mind when it comes to use these tools in post‐introduction observation of new technologies.Conclusions  At present, the most appropriate data collection method for conducting post‐introduction observation of new technologies is the use of prospective clinical registries. Electronic clinical records may replace clinical registries in the near future, but currently there are still many doubts as to the quality of the information retrieved.