bluuebunny/crossref_metadata_2025_split huggingface dataset:
Innovative empirical approaches for inferring climate‐warming impacts on plants in remote areas
Authors: De Frenne Pieter 
Published: August 2014

SummaryThe prediction of the effects of climate warming on plant communities across the globe has become a major focus of ecology, evolution and biodiversity conservation. However, many of the frequently used empirical approaches for inferring how warming affects vegetation have been criticized for decades. In addition, methods that require no electricity may be preferred because of constraints of active warming, e.g. in remote areas. Efforts to overcome the limitations of earlier methods are currently under development, but these approaches have yet to be systematically evaluated side by side. Here, an overview of the benefits and limitations of a selection of innovative empirical techniques to study temperature effects on plants is presented, with a focus on practicality in relatively remote areas without an electric power supply. I focus on methods for: ecosystem aboveground and belowground warming; a fuller exploitation of spatial temperature variation; and long‐term monitoring of plant ecological and microevolutionary changes in response to warming. An evaluation of the described methodological set‐ups in a synthetic framework along six axes (associated with the consistency of temperature differences, disturbance, costs, confounding factors, spatial scale and versatility) highlights their potential usefulness and power. Hence, further developments of new approaches to empirically assess warming effects on plants can critically stimulate progress in climate‐change biology.
Using Bayesian Models to Assess the Effects of Under‐reporting of Cannabis Use on the Association with Birth Defects, National Birth Defects Prevention Study, 1997–2005
Authors: van Gelder Marleen M. H. J. , Donders A. Rogier T. , Devine Owen , Roeleveld Nel , Reefhuis Jennita ,   National Birth Defects Prevention Study
Published: August 2014

AbstractBackgroundStudies on associations between periconceptional cannabis exposure and birth defects have mainly relied on self‐reported exposure. Therefore, the results may be biased due to under‐reporting of the exposure. The aim of this study was to quantify the potential effects of this form of exposure misclassification.MethodsUsing multivariable logistic regression, we re‐analysed associations between periconceptional cannabis use and 20 specific birth defects using data from the National Birth Defects Prevention Study from 1997–2005 for 13 859 case infants and 6556 control infants. For seven birth defects, we implemented four Bayesian models based on various assumptions concerning the sensitivity of self‐reported cannabis use to estimate odds ratios (ORs), adjusted for confounding and under‐reporting of the exposure. We used information on sensitivity of self‐reported cannabis use from the literature for prior assumptions.ResultsThe results unadjusted for under‐reporting of the exposure showed an association between cannabis use and anencephaly (posterior OR 1.9 [95% credible interval (CRI) 1.1, 3.2]) which persisted after adjustment for potential exposure misclassification. Initially, no statistically significant associations were observed between cannabis use and the other birth defect categories studied. Although adjustment for under‐reporting did not notably change these effect estimates, cannabis use was associated with esophageal atresia (posterior OR 1.7 [95% CRI 1.0, 2.9]), diaphragmatic hernia (posterior OR 1.8 [95% CRI 1.1, 3.0]), and gastroschisis (posterior OR 1.7 [95% CRI 1.2, 2.3]) after correction for exposure misclassification.ConclusionsUnder‐reporting of the exposure may have obscured some cannabis‐birth defect associations in previous studies. However, the resulting bias is likely to be limited.
Variations in resting frontal alpha asymmetry between high‐ and low‐neuroticism females across the menstrual cycle
Authors: Huang Yamei , Zhou Renlai , Cui Hong , Wu Mengying , Wang Qingguo , Zhao Yan , Liu Yanfeng 
Published: August 2014

AbstractResting frontal alpha asymmetry measures the relative activation intensity across the left and right frontal regions that represent emotional experience. Here, the focus is on levels of alpha asymmetry between high‐ and low‐neuroticism females across the menstrual cycle. Resting alpha asymmetry in healthy females who scored high or low on neuroticism was assessed during the menstrual phase, the late follicular phase, and the midlate luteal phase. High‐neuroticism females exhibited lower relative left prefrontal activity than did low‐neuroticism females during the midlate luteal phase, as indexed by alpha1 and alphaTotal asymmetry scores at the prefrontal electrode positions (FP1/2). EEG results demonstrate that the resting frontal alpha asymmetry of high‐ and low‐neuroticism females was moderated by the menstrual cycle, and high‐neuroticism females should pay particular attention to their emotional experience during the midlate luteal phase.
Feasibility of 8‐OHdG formation and hOGG1 induction in PBMCs for assessing oxidative DNA damage in the lung of COPD patients
Authors: Yang Shifang , Wu Hongxu , Zhao Junling , Wu Xiaojie , Zhao Jianping , Ning Qin , Xu Yongjian , Xie Jungang 
Published: August 2014

AbstractBackground and objectiveOxidative stress has long been recognized to play a role in chronic obstructive pulmonary disease (COPD); however, approaches for assessing oxidative stress are lacking. The objective of this study was to address the feasibility of measuring 8‐oxo‐7, 8‐dihydro‐2′‐deoxyguanosine (8‐OHdG) formation and human 8‐oxoguanine DNA glycosylase (hOGG1) induction in peripheral blood mononuclear cell (PBMC) to assess oxidative deoxyribonucleic acid (DNA) damage in the lung of smoking COPD patients.MethodsPBMC were obtained from 412 participants including 129 smokers with COPD, 143 healthy smokers and 140 healthy non‐smokers. Lung tissue specimens and PBMC were obtained from smoker COPD (n = 12), healthy smokers (n = 12) and healthy non‐smokers (n = 10). 8‐OHdG and hOGG1 were detected, and correlation analysis was conducted for assessing the feasibility.ResultsOxidative DNA damage (8‐OHdG formation) along with impaired induction of hOGG1 expression in the lung was a prominent feature for smokers COPD patients. PBMC originated from smokers COPD patients also displayed similar features to that of lung tissues. Correlation analysis suggests that PBMC could be used as a surrogate for oxidative DNA damage in lung of smokers COPD patients. Indeed, 8‐OHdG levels in PBMC DNA were negatively correlated with lung function, while hOGG1 induction in PBMC was associated with improved lung function in smokers COPD patients.ConclusionsCOPD patients manifest oxidative DNA damage of 8‐OHdG along with impaired hOGG1 expression in the lung, whereas 8‐OHdG formation and hOGG1 induction in PBMC could be a biomarker of oxidative DNA damage in the lung.
Application of leukotriene B4 and reflectance confocal microscopy as a noninvasivein vivomodel to study the dynamics of skin inflammation
Authors: Peppelman M. , Wolberink E. A. W. , Gerritsen M.‐J. P. , van de Kerkhof P. C. M. , van Erp P. E. J. 
Published: August 2014

BackgroundApplication of leukotriene B4 (LTB4) is an establishedin vivomodel that locally induces skin inflammation. Currently in this model, a biopsy is inevitable.In vivoreflectance confocal microscopy (RCM), a noninvasive imaging technique, could overcome this limitation. To find out to what extentRCMmay be anin vivoinvestigative and diagnostic tool in neutrophilic conditions, we studied the dynamics of polymorphonuclear leukocytes (PMN) migration from dermis to stratum corneum using an establishedLTB4 model.MethodsLeukotriene B4 was topically applied on the skin of the lower back of seven volunteers. The skin sites were evaluated byRCMfor three consecutive days with a 24 h time interval. For histological correlation, 3‐mm punch biopsies were obtained. The tissue sections were hematoxylin–eosin and immunohistochemical stained. Minimal and average epidermal thickness was measured.ResultsReflectance confocal microscopy imaging showed highly reflective ill‐defined particles with a granular content throughout the epidermis 24 h after application ofLTB4. Over time, the appearance of these cells changed throughout the epidermis. Epidermal thickness increased over time, and the measurements based on theRCMimages corresponded very well with the histological images.ConclusionsReflectance confocal microscopy was able to visualizePMNmigration, accumulation, and degeneration over time in the usedLTB4 model. The noninvasive character and the possibility to obtain multiplein vivoimages from the same location over time make thatRCMin combination with this model a useful tool to study the dynamics and function ofPMNin inflammatory processes in the skin.
The geographic and demographic scope of shared sanitation: an analysis of national survey data from low‐ and middle‐income countries
Authors: Heijnen Marieke , Rosa Ghislaine , Fuller James , Eisenberg Joseph N. S. , Clasen Thomas 
Published: August 2014

AbstractObjectiveA large and growing proportion of the world's population rely on shared sanitation facilities that have historically been excluded from international targets due to concerns about acceptability, hygiene and access. In connection with a proposed change in such policy, we undertook this study to describe the prevalence and scope of households that report relying on shared sanitation and to characterise them in terms of selected socio‐economic and demographic covariates.MethodsWe extracted data from the most recent national household surveys of 84 low‐ and middle‐income countries from Demographic and Health Surveys and Multiple Indicator Cluster Surveys. We describe the prevalence of shared sanitation and explore associations between specified covariates and reliance on shared sanitation using log‐binomial regression.ResultsWhile household reliance on any type of shared sanitation is relatively rare in Europe (2.5%) and the Eastern Mediterranean (7.7%), it is not uncommon in the Americas (14.2%), Western Pacific (16.4%) and South‐East Asia (31.3%), and it is most prevalent in Africa (44.6%) where many shared facilities do not meet the definition of ‘improved’ even if they were not shared (17.7%). Overall, shared sanitation is more common in urban (28.6%) than in rural settings (25.9%), even after adjusting for wealth. While results vary geographically, people who rely on shared sanitation tend to be poorer, reside in urban areas and live in households with more young children and headed by people with no formal education. Data from 21 countries suggest that most sharing is with neighbours and other acquaintances (82.0%) rather than the public.ConclusionsThe determinants of shared sanitation identified from these data suggest potential confounders that may explain the apparent increased health risk from sharing and should be considered in any policy recommendation. Both geographic and demographic heterogeneity indicate the need for further research to support a change in policies.
Metabolomic analysis of platelets during storage: a comparison between apheresis‐ and buffy coat–derived platelet concentrates
Authors: Paglia Giuseppe , Sigurjónsson Ólafur E. , Rolfsson Óttar , Hansen Morten Bagge , Brynjólfsson Sigurður , Gudmundsson Sveinn , Palsson Bernhard O. 
Published: August 2014

BackgroundPlatelet concentrates (PCs) can be prepared using three methods: platelet (PLT)‐rich plasma, apheresis, and buffy coat. The aim of this study was to obtain a comprehensive data set that describes metabolism of buffy coat–derived PLTs during storage and to compare it with a previously published parallel data set obtained for apheresis‐derived PLTs.Study Design and MethodsDuring storage we measured more than 150 variables in 8 PLT units, prepared by the buffy coat method. Samples were collected at seven different time points resulting in a data set containing more than 8000 measurements. This data set was obtained by combining a series of standard quality control assays to monitor the quality of stored PLTs and a deep coverage metabolomics study using liquid chromatography coupled with mass spectrometry.ResultsStored PLTs showed a distinct metabolic transition occurring 4 days after their collection. The transition was evident in PLT produced by both production methods. Apheresis‐derived PLTs showed a clearer phenotype of PLT activation during early days of storage. The activated phenotype of apheresis PLTs was accompanied by a higher metabolic activity, especially related to glycolysis and the tricarboxylic acid cycle. Moreover, the extent of the activation differed between bags resulting in interbag variability in the storage lesion of apheresis‐prepared PLTs. This may be related to donor‐related polymorphism.ConclusionThis study demonstrated two discrete metabolic phenotypes in stored PLTs prepared with both apheresis and buffy coat methods. PLT activation occurs during the first metabolic phenotype and might lead to a low reproducibility of the apheresis PCs.
Blood reference materials from macaques infected with variant Creutzfeldt‐Jakob disease agent
Authors: McDowell Kristy L. , Nag Nabanita , Franco Zulmarie , Bu Ming , Piccardo Pedro , Cervenak Juraj , Deslys Jean‐Philippe , Comoy Emmanuel , Asher David M. , Gregori Luisa 
Published: August 2014

BackgroundVariant Creutzfeldt‐Jakob disease (vCJD) is a fatal neurodegenerative infection that can be transmitted by blood and blood products from donors in the latent phase of the disease. Currently, there is no validated antemortem vCJD blood screening test. Several blood tests are under development. Any useful test must be validated with disease‐relevant blood reference panels.Study Design and MethodsTo generate blood reference materials, we infected four cynomolgus macaques with macaque‐adapted vCJD brain homogenates. Blood was collected throughout the preclinical and clinical phases of infection. In parallel, equivalent blood was collected from one uninfected macaque. For each blood collection, an aliquot was stored as whole blood and the remainder was separated into components. Aliquots of plasma from terminally ill macaques were assayed for the presence of PrPTSE with the protein misfolding cyclic amplification (PMCA) method. Infectivity of the macaque brain homogenate used to infect macaques was titrated in C57BL/6 and RIII J/S inbred wild‐type mice.ResultsWe sampled blood 19 times from the inoculated monkeys at various stages of the disease over a period of 29 months, generating liters of vCJD‐infected macaque blood. vCJD was confirmed in all inoculated macaques. After PMCA, PrPTSE was detected in plasma from infected monkeys, but not from uninfected animals. Both mouse models were more sensitive to infection with macaque‐adapted vCJD agent than to primary human vCJD agent.ConclusionThe macaque vCJD blood panels generated in this study provide a unique resource to support vCJD assay development and to characterize vCJD infectivity in blood.
THE TREES, MY LUNGS: SELF PSYCHOLOGY AND THE NATURAL WORLD AT AN AMERICAN BUDDHIST CENTER
Authors: Capper Daniel 
Published: August 2014

AbstractThis study employs ethnographic field data to trace a dialogue between the self‐psychological concept of the self object and experiences regarding the concept of “interbeing” at a Vietnamese Buddhist monastery in the United States. The dialogue develops an understanding of human experiences with the nonhuman natural world which are tensive, liminal, and nondual. From the dialogue I find that the self object concept, when applied to this form of Buddhism, must be inclusive enough to embrace relationships with animals, stones, and other natural forms. The dialogue further delineates a self‐psychological methodology for examining religions in their interactions with natural forms.
HERE AND NOW: DISCOVERING THE SACRED WITH ENTHEOGENS
Authors: Richards William A. 
Published: August 2014

AbstractRenewed research with entheogens (psychedelic substances) has been able to facilitate the occurrence of mystical forms of consciousness in healthy volunteers with a high degree of reliability. This article explores the potential significance of this development for religious scholars, especially those interested in the study of mysticism. The definition of “mystical consciousness” employed in this research is presented and differentiated from visionary/archetypal and other types of alternative mental states. The ways in which entheogens may be employed with skill and maximum safety are discussed. Implications for clarifying confusion in the study of mysticism are considered, along with suggestions for future religious research on this frontier of knowledge.
GOD, CHRIST, AND ANIMALS
Authors: Fergusson David 
Published: August 2014

AbstractOne of the most significant contributions to the field in recent times, David Clough's work On Animals: Volume 1, Systematic Theology, should ensure that theologies of creation, redemption, and eschatological fulfillment give proper attention to animals. In a landmark study, he draws upon resources in Scripture and tradition to present a systematic theology that is alert to the place of animals in the divine economy. Amidst his relentless criticism of all forms of anthropocentrism, however, it is asked whether some unresolved tensions emerge in relation to the traditional doctrine of God, the use of the category of the “personal” in theology, and the incarnation of the Word of God as a human creature.
Development of a golden beam data set for the commissioning of a proton double‐scattering system in a pencil‐beam dose calculation algorithm
Authors: Slopsema R. L. , Lin L. , Flampouri S. , Yeung D. , Li Z. , McDonough J. E. , Palta J. 
Published: August 2014

Purpose:The purpose of this investigation is to determine if a single set of beam data, described by a minimal set of equations and fitting variables, can be used to commission different installations of a proton double‐scattering system in a commercial pencil‐beam dose calculation algorithm.Methods:The beam model parameters required to commission the pencil‐beam dose calculation algorithm (virtual and effective SAD, effective source size, and pristine‐peak energy spread) are determined for a commercial double‐scattering system. These parameters are measured in a first room and parameterized as function of proton energy and nozzle settings by fitting four analytical equations to the measured data. The combination of these equations and fitting values constitutes the golden beam data (GBD). To determine the variation in dose delivery between installations, the same dosimetric properties are measured in two additional rooms at the same facility, as well as in a single room at another facility. The difference between the room‐specific measurements and the GBD is evaluated against tolerances that guarantee the 3D dose distribution in each of the rooms matches the GBD‐based dose distribution within clinically reasonable limits. The pencil‐beam treatment‐planning algorithm is commissioned with the GBD. The three‐dimensional dose distribution in water is evaluated in the four treatment rooms and compared to the treatment‐planning calculated dose distribution.Results:The virtual and effective SAD measurements fall between 226 and 257 cm. The effective source size varies between 2.4 and 6.2 cm for the large‐field options, and 1.0 and 2.0 cm for the small‐field options. The pristine‐peak energy spread decreases from 1.05% at the lowest range to 0.6% at the highest. The virtual SAD as well as the effective source size can be accurately described by a linear relationship as function of the inverse of the residual energy. An additional linear correction term as function of RM‐step thickness is required for accurate parameterization of the effective SAD. The GBD energy spread is given by a linear function of the exponential of the beam energy. Except for a few outliers, the measured parameters match the GBD within the specified tolerances in all of the four rooms investigated. For a SOBP field with a range of 15 g/cm2 and an air gap of 25 cm, the maximum difference in the 80%–20% lateral penumbra between the GBD‐commissioned treatment‐planning system and measurements in any of the four rooms is 0.5 mm.Conclusions:The beam model parameters of the double‐scattering system can be parameterized with a limited set of equations and parameters. This GBD closely matches the measured dosimetric properties in four different rooms.
Comparative Systems Biology Analysis To Study the Mode of Action of the Isothiocyanate Compound Iberin on Pseudomonas aeruginosa
Authors: Tan Sean Yang-Yi , Liu Yang , Chua Song Lin , Vejborg Rebecca Munk , Jakobsen Tim Holm , Chew Su Chuen , Li Yingying , Nielsen Thomas E. , Tolker-Nielsen Tim , Yang Liang , Givskov Michael 
Published: August 2014

ABSTRACT

Food is now recognized as a natural resource of novel antimicrobial agents, including those that target the virulence mechanisms of bacterial pathogens. Iberin, an isothiocyanate compound from horseradish, was recently identified as a quorum-sensing inhibitor (QSI) of the bacterial pathogen
Pseudomonas aeruginosa
. In this study, we used a comparative systems biology approach to unravel the molecular mechanisms of the effects of iberin on QS and virulence factor expression of
P. aeruginosa
. Our study shows that the two systems biology methods used (i.e., RNA sequencing and proteomics) complement each other and provide a thorough overview of the impact of iberin on
P. aeruginosa
. RNA sequencing-based transcriptomics showed that iberin inhibits the expression of the GacA-dependent small regulatory RNAs RsmY and RsmZ; this was verified by using
gfp
-based transcriptional reporter fusions with the
rsmY
or
rsmZ
promoter regions. Isobaric tags for relative and absolute quantitation (iTRAQ) proteomics showed that iberin reduces the abundance of the LadS protein, an activator of GacS. Taken together, the findings suggest that the mode of QS inhibition in iberin is through downregulation of the Gac/Rsm QS network, which in turn leads to the repression of QS-regulated virulence factors, such as pyoverdine, chitinase, and protease IV. Lastly, as expected from the observed repression of small regulatory RNA synthesis, we also show that iberin effectively reduces biofilm formation. This suggests that small regulatory RNAs might serve as potential targets in the future development of therapies against pathogens that use QS for controlling virulence factor expression and assume the biofilm mode of growth in the process of causing disease.