bluuebunny/crossref_metadata_2025_split huggingface dataset:
Labeling Lipids for Imaging in Fixed Cells: Figure 1.
Authors: Schultz Carsten , Neef Anne B. , Gadella Theodorus W. , Goedhart Joachim 
Published: July 2010

INTRODUCTIONFluorescently tagged lipid-binding domains have become a popular tool to image lipids that are involved in intracellular signaling processes. The readout usually involves the translocation of the lipid-binding domain from the cytosol or nucleosol to the membrane of interest, or vice versa. Unfortunately, this method seems to work predominantly for lipids in the plasma membrane, whereas lipids such as phosphatidylinositol 4,5-bisphosphate (PIP2) are not recognized in the membranes of the endoplasmic reticulum or the Golgi. Very recently, we developed an alternative way of localizing a lipid of interest by fluorescent labeling of minimally modified lipid derivatives using a single specific chemical reaction. This protocol describes how to directly label lipids in fixed cells for lipid location analyses.
Imaging Lipids in Living Cells
Authors: Schultz Carsten , Neef Anne B. , Gadella Theodorus W. , Goedhart Joachim 
Published: July 2010

INTRODUCTIONThe investigation of lipids in living cells is one of the underdeveloped areas in cell biology. Although it is possible to analyze the global lipid composition of a cell type, fractionation of the various types of membranes from cells is extraordinarily difficult, mainly because most membranes appear to be in contact with each other. Therefore, we know the lipid components, but we have a difficult time finding out their exact position, how dynamically they change location, and how rapidly they are metabolized. Imaging lipids in cells seems to be the obvious solution to the problem. The most common way to image molecules is by the artificial addition of a fluorescent tag. The use of fluorescent proteins has become the mainstay of protein imaging, but this method is, of course, not suitable for small molecules such as lipids. Unfortunately, the fluorescent tag is usually as large as the lipid and is therefore likely to have a severe influence on lipid location and metabolism. To circumvent this problem, two solutions have been developed--namely, the use of fluorescently labeled proteins that specifically recognize lipids and a chemical method to introduce the fluorescent tag inside the cell. This article describes procedures necessary to image lipids by fluorescently tagged lipid-binding domains and by labeling lipid derivatives in fixed and living cells.
Ethylene Signaling Regulates Accumulation of the FLS2 Receptor and Is Required for the Oxidative Burst Contributing to Plant Immunity
Authors: Mersmann Sophia , Bourdais Gildas , Rietz Steffen , Robatzek Silke 
Published: July 2010

Abstract
Reactive oxygen species (ROS) are potent signal molecules rapidly generated in response to stress. Detection of pathogen-associated molecular patterns induces a transient apoplastic ROS through the function of the NADPH respiratory burst oxidase homologs D (RbohD). However, little is known about the regulation of pathogen-associated molecular pattern-elicited ROS or its role in plant immunity. We investigated ROS production triggered by bacterial flagellin (flg22) in Arabidopsis (Arabidopsis thaliana). The oxidative burst was diminished in ethylene-insensitive mutants. Flagellin Sensitive2 (FLS2) accumulation was reduced in etr1 and ein2, indicating a requirement of ethylene signaling for FLS2 expression. Multiplication of virulent bacteria was enhanced in Arabidopsis lines displaying altered ROS production at early but not late stages of infection, suggesting an impairment of preinvasive immunity. Stomatal closure, a mechanism used to reduce bacterial entry into plant tissues, was abolished in etr1, ein2, and rbohD mutants. These results point to the importance of flg22-triggered ROS at an early stage of the plant immune response.
Cytodiagnosis through use of a z‐axis video by volunteer observers: a promising tool for external quality assessment
Authors: Yamashiro K. , Tagami M. , Azuma K. , Nakamura A. , Kato O. , Taira K. , Azuma M. , Takeda H. , Suzuki H. 
Published: June 2010

K. Yamashiro, M. Tagami, K. Azuma, A. Nakamura, O. Kato, K. Taira, M. Azuma, H. Takeda and H. Suzuki Cytodiagnosis through use of a z‐axis video by volunteer observers: a promising tool for external quality assessment Objective:  This study examined whether cytological diagnosis through the use of a video, which shows the changing depth of focus in the microscopic field, described as a z‐axis video, is useful compared with a still image.Methods:  From 17 cytology preparations of fine needle aspiration of the breast, we made six z‐axis videos per case. A frame exhibiting the characteristic features was then extracted from each video and saved as a representative still image. One hundred and twenty‐eight volunteer cytotechnologists were randomly divided into two groups of video observers and still image observers. The participants were asked to make a diagnosis of benign, indeterminate, suspicious or malignant without having any clinical information other than the age of the patient. Diagnoses were categorized as ‘recommended’ or ‘unacceptable’ according to degree of correlation with histology.Results:  The number of definitive diagnoses of ‘benign’ or ‘malignant’ were increased in video observers, and indeterminate or suspicious categories were decreased (P = 0.013). The distribution of diagnostic categories in three of the 17 cases was significantly different; the distribution in the remaining cases was similar between the two groups. The z‐axis video observers may have selected the definite diagnoses with confidence because they observed valuable microscopic findings by ‘focusing through observation’. The average number of ‘recommended’ diagnoses by individual observers was significantly higher in the video observer group than in the still image observer group (P = 0.016). In contrast, the average number of ‘unacceptable’ diagnoses was significantly lower (P = 0.019).Conclusions:  A z‐axis video is easy to obtain and is therefore expected to become a powerful diagnostic modality for the external quality assessment of clinical cytology and even in the field of primary cytodiagnosis.
Biases in the analysis of stable isotope discrimination in food webs
Authors: Auerswald Karl , Wittmer Maximilian H. O. M. , Zazzo Antoine , Schäufele Rudi , Schnyder Hans 
Published: June 2010

Summary 1. Recently, Caut, Angulo & Courchamp (2009, Journal of Applied Ecology) published a review on diet‐tissue isotopic shifts in animals. They concluded that diet‐tissue shifts are influenced by the isotopic composition of the diet for both 13C and 15N in a wide range of animal taxa. 2. We suggest that the conclusion of Caut, Angulo & Courchamp is in error, and provide a discussion of sources of error in the assessment of diet‐tissue discrimination. 3. Errors in the derivation of diet‐tissue shifts include imprecise definitions, mathematical artefacts and invalid statistical analysis. It is likely that the work also suffers from experimental bias. The mathematical artefacts and statistical invalidity result from using the same variable (diet isotopic composition) in the independent and dependent variable for regression analysis and failure to correct for the resulting bias. Experimental bias can result from the incomplete turnover of body pools after diet switches or during natural fluctuations in diet isotope composition. Unfortunately, the main sources of error work in the same direction, strengthening the biased relationship between the diet‐tissue shift and diet isotope composition. Therefore, the analysis of Caut et al. (2009) does not provide proof of a relationship between diet‐tissue shift and diet isotope composition. 4.
Synthesis and application. Future work on diet‐tissue discrimination factors should (i) follow the mathematical rules resulting from how isotope data are presented, (ii) be based on appropriate statistics analysis that avoids or corrects for spurious self‐correlations, and (iii) consider possible complications associated with the presence of slowly turning‐over stores and non‐equilibrating ‘dead’ body pools.
Trophic experiments to estimate isotope discrimination factors
Authors: Caut Stephane , Angulo Elena , Courchamp Franck , Figuerola Jordi 
Published: June 2010

Summary 1. In Caut, Angulo & Courchamp (2008a) rats were fed with experimental diets of distinct isotopic values (δ13C and δ15N) in order to infer the discrimination factors. We showed negative relationships between discrimination factors and diet isotopic values. In Caut, Angulo & Courchamp (2009), our aim was to generalize these relationships to other taxonomic groups with a view to providing ecologists with a general and flexible method to obtain discrimination factors for diet reconstruction studies when difficult to obtain otherwise. 2.
Perga & Grey (2010) claims that there is an artefact of experimental design (due to protein contents) and partly reanalyzes our data, taking into account the type of diet (mixed or not; carnivorous, omnivorous or herbivorous). However, (i) the role of protein content through isotopic routing is not clear; (ii) a reanalysis of our data shows that the relationships between discrimination factors and diet isotopic values remain significant even when following Perga’s suggestions. 3.
Auerswald et al. (2010) criticized the imprecise definitions, mathematical artefacts and invalid statistical analysis of Caut, Angulo & Courchamp (2009). However, (i) their arguments are not new; they challenge the use of stable isotope in ecological trophic studies in general, and lack both alternative suggestions and ecological perspective; (ii) none of their statistical and mathematical objections has a significant effect on the results. 4.
Synthesis and applications. Neither reply reflects the current context of debate. The complementarity between experimental studies and their application in field studies is indispensable for the use of stable isotopes in ecology. Protocols should be very well assessed in order to represent field conditions with accuracy. Further analyses are necessary to remove some of the flaws in the use of stable isotopes (carrying out an in‐depth analysis of isotopic routing, turnover, and dynamic during trophic experiments to ensure accurate attainment of equilibrium), but none of the issues raised by Perga & Grey (2010) and Auerswald et al. (2010) alter our main conclusions.
Biological roles of translesion synthesis DNA polymerases in eubacteria
Authors: Andersson Dan I. , Koskiniemi Sanna , Hughes Diarmaid 
Published: June 2010

SummaryBiological systems are strongly selected to maintain the integrity of their genomes by prevention and repair of external and internal DNA damages. However, some types of DNA lesions persist and might block the replication apparatus. The universal existence of specialized translesion synthesis DNA polymerases (TLS polymerases) that can bypass such lesions in DNA implies that replication blockage is a general biological problem. We suggest that the primary function for which translesion synthesis polymerases are selected is to rescue cells from replication arrest at lesions in DNA, a situation that, if not amended, is likely to cause an immediate and severe reduction in cell fitness and survival. We will argue that the mutagenesis observed during translesion synthesis is an unavoidable secondary consequence of this primary function and not, as has been suggested, an evolved mechanism to increase mutation rates in response to various stresses. Finally, we will discuss recent data on additional roles for translesion synthesis polymerases in the formation of spontaneous deletions and in transcription‐coupled TLS, where the coupling of transcription to TLS is proposed to allow the rescue of the transcription machinery arrested at DNA lesions.
Spatiotemporal expression pattern of an encephalopsin orthologue of the sea urchin Hemicentrotus pulcherrimus during early development, and its potential role in larval vertical migration
Authors: Ooka Shioh , Katow Tomoko , Yaguchi Shunsuke , Yaguchi Junko , Katow Hideki 
Published: July 2010

We have cloned and studied Hp‐ECPN, an encephalopsin orthologue of the sea urchin Hemicentrotus pulcherrimus. Hp‐ecpn cDNA was produced and found to contain a 1461‐bp open reading frame that encodes 486 amino acids. Accumulation of Hp‐ecpn mRNA and protein expression occurred at the 14 h postfertilization (hpf) swimming blastula stage and thereafter. The Hp‐ECPN protein was N‐glycosylated, and the amino acid sequence was similar to that of vertebrate encephalopsins. Whole‐mount immunohistochemistry revealed the presence of Hp‐ECPN in cells (ECPN cells) that appeared initially around the tip of the archenteron in 20 hpf early gastrulae. By the 54 hpf pluteus stage, ECPN cells had spread through the aboral ectoderm, and, by the eight‐arm pluteus stage, were restricted to the tips of the larval arms and the posterior end of the body. The number of ECPN cells increased under conditions of continuous light, but decreased under continuous dark. Knockdown of Hp‐ecpn mRNA using morpholino antisense oligonucleotides decreased the number of ECPN cells considerably, and inhibited the vertical swimming of the larvae. This suggested that Hp‐ECPN plays a role in photosensitive larval swimming vertical migration. In adult tissues, the ECPN cells were detected exclusively in tube feet.
Laterality of nephrocalcinosis in kidney stone formers with severe hypocitraturia
Authors: Le Jesse D. , Eisner Brian H. , Tseng Timothy Y. , Chi Thomas , Stoller Marshall L. 
Published: June 2010

Study Type – Aetiology (case series) Level of Evidence 4 What’s known on the subject? and What does the study add? Systemic urinary stone‐forming conditions such as hypocitraturia or cystinuria should theoretically lead to symmetric and diffuse stone formation. Small studies have shown that some patients with such conditions produce stones primarily on one side. No studies, however, have attempted to quantify the frequency at which such patients form stones asymmetrically.This study demonstrates that despite having a severe systemic condition such as hypocitraturia, patients frequently have asymmetric and focal nephrocalcinosis. This suggests that additional intrinsic local factors such as renal perfusion or vascular injury must also play a role in stone formation.OBJECTIVE To examine the hypothesis that the distribution of nephrocalcinosis in patients with severe hypocitraturia should be symmetric.PATIENTS AND METHODS Patients with profound hypocitraturia defined as a 24‐h urine citrate <50 mg at the time of initial presentation were identified from the metabolic stone clinic database at our academic medical center. Two independent blinded reviewers evaluated all of the abdominal radiographs for the segmental distribution of macroscopic nephrocalcinosis.RESULTS A total of 44 patients met study criteria, with an equal distribution of males and females and a mean age of 55.4 ± 13.7 years. Mean urinary citrate was 28 ± 11 mg/day. Nephrocalcinosis was present in at least one renal segment in 22 patients (50%). Of the 22 patients with nephrocalcinosis, 9 patients (41%) had unilateral nephrocalcinosis and 13 patients (59%) had bilateral nephrocalcinosis. Of the 35 kidneys with nephrocalcinosis, 14 kidneys (40%) had nephrocalcinosis in only one renal segment, 13 kidneys (37%) had nephrocalcinosis in two segments and eight kidneys (23%) had nephrocalcinosis involving all three segments.CONCLUSIONS Despite the systemic nature of severe hypocitraturia, nephrocalcinosis is frequently asymmetric and focal in nature. This suggests that local factors intrinsic to the renal medullary interstitium, such as vascular injury, must play a role in the formation of nephrocalcinosis. Further study to elucidate these intrinsic local factors may further improve the treatment and prevention of urinary stone disease.
Detection of urinary leakage after radical retropubic prostatectomy by contrast enhanced ultrasound – do we still need conventional retrograde cystography?
Authors: Schoeppler Gita M. , Buchner Alexander , Zaak Dirk , Khoder Wael , Staehler Michael , Stief Christian G. , Reiser Maximilian F. , Clevert Dirk‐Andre 
Published: June 2010

Study Type – Diagnostic (exploratory cohort) Level of Evidence 2bINTRODUCTION To prospectively evaluate the accuracy of transvesical contrast‐enhanced ultrasound (CEUS) as an alternative method for the detection of anastomotic leakage after radical retropubic prostatectomy (RRP) in comparison with the current standard method of conventional retrograde cystography (CG).PATIENTS AND METHODS Forty‐three patients underwent RRP for histologically proven localized prostate cancer. The vesico‐urethral anastomosis was evaluated 8 days after RRP by CG and CEUS. Any peri‐anastomotic leakage was assessed and determined in CG and CEUS as follows: no extravasation (EV), small leakage (≤0.5 cm), moderate leakage (>0.5 cm to ≤2 cm), large leakage (>2 cm diameter of EV seen).RESULTS In total, 21 (49%) patients showed a watertight anastomosis. Ten (23%), two (4.7%) and ten (23%) patients showed a small, intermediate and large EV, respectively. In 31 cases (72%) there was 100% agreement of CG and CEUS for detection of no, moderate and large EV, respectively. In nine cases a small and in two cases a moderate EV was categorized as watertight anastomosis by CEUS. Only in one case did CG detect a small EV where a large EV was detected in CEUS. The agreement between both methods was 95% for detecting absence or large leakages.CONCLUSION CEUS is a promising imaging modality that seems to be equivalent to CG for detecting the presence of a large anastomotic leakage that is clinically relevant for postoperative persistence of the indwelling catheter. CEUS could be a cheap and time‐saving alternative to the CG without exposure of the patient to radiation.
A Spatial Analysis System for Integrating Data, Methods and Models on Environmental Risks and Health Outcomes
Authors: Tiwari Chetan , Rushton Gerard 
Published: June 2010

AbstractIntegrating data on health outcomes with methods of disease mapping and spatially explicit models of environmental contaminants are important aspects of environmental health surveillance. In this article, we describe a modular, web‐based spatial analysis system that uses GIS, spatial analysis methods and software services delivered over computer networks to achieve this end. The Environmental Health Surveillance System (EHSS) is a prototype system that is designed to serve three purposes: a secure environment for producing maps of disease outcomes from individual‐level data while preserving privacy; an automated process of linking environmental data, environmental models, and GIS tasks like geocoding for the purposes of estimating individual exposures to environmental contaminants; and mechanisms to visualize the spatial patterns of disease outcomes via Web‐based mapping interfaces and interactive tools like Google Earth.
Fiscal Policy Shocks in the Euro Area and the US: An Empirical Assessment*
Authors: Burriel Pablo , De Castro Francisco , Garrote Daniel , Gordo Esther , Paredes Joan , Pérez Javier J. 
Published: June 2010

AbstractWe analyse the impact of fiscal policy shocks in the euro area as a whole, using a newly‐available quarterly data set of fiscal variables for the period 1981–2007. To allow for comparability with previous results on euro‐area countries and the US, we use a standard structural vector autoregressive (VAR) framework, and study the impact of aggregated and disaggregated government spending and net‐tax shocks. In addition, to frame euro‐area results, we apply the same methodology for the same sample period to US data. We also explore the sensitivity of the results to the inclusion of variables aiming to control for underlying financial and fiscal conditions. The main new findings are that: expansionary fiscal shocks have a short‐term positive impact on GDP and private consumption, with government spending shocks entailing, in general, higher effects on economic activity than (net) tax reductions; output multipliers to government expenditure shocks are of similar size in the euro area and in the US; the persistence of a fiscal spending shock is higher in the US than in the euro area, which appears to be related to military spending in the US; and fiscal multipliers have increased over the recent past in both geographical areas.
Physical Activity Over the Life Course and Its Association with Cognitive Performance and Impairment in Old Age
Authors: Middleton Laura E. , Barnes Deborah E. , Lui Li‐Yung , Yaffe Kristine 
Published: July 2010

OBJECTIVE: To determine how physical activity at various ages over the life course is associated with cognitive impairment in late life.DESIGN: Cross‐sectional study.SETTING: Four U.S. sites.PARTICIPANTS: Nine thousand three hundred forty‐four women aged 65 and older (mean 71.6) who self‐reported teenage, age 30, age 50, and late‐life physical activity.MEASUREMENTS: Logistic regression was used to determine the association between physical activity status at each age and likelihood of cognitive impairment (modified Mini‐Mental State Examination (mMMSE) score >1.5 standard deviations below the mean, mMMSE score≤22). Models were adjusted for age, education, marital status, diabetes mellitus, hypertension, depressive symptoms, smoking, and body mass index.RESULTS: Women who reported being physically active had a lower prevalence of cognitive impairment in late life than women who were inactive at each time (teenage: 8.5% vs 16.7%, adjusted odds ratio (AOR)=0.65, 95% confidence interval (CI)=0.53–0.80; age 30: 8.9% vs 12.0%, AOR=0.80, 95% CI=0.67–0.96); age 50: 8.5% vs 13.1%, AOR=0.71, 95% CI=0.59–0.85; old age: 8.2% vs 15.9%, AOR=0.74, 95% CI=0.61–0.91). When the four times were analyzed together, teenage physical activity was most strongly associated with lower odds of late‐life cognitive impairment (OR=0.73, 95% CI=0.58–0.92). However, women who were physically inactive as teenagers and became active in later life had lower risk than those who remained inactive.CONCLUSIONS: Women who reported being physically active at any point over the life course, especially as teenagers, had a lower likelihood of cognitive impairment in late life. Interventions should promote physical activity early in life and throughout the life course.
Epidermal growth factor receptor tyrosine kinase inhibitors induce CCL2 and CCL5 via reduction in IL‐1R2 in keratinocytes
Authors: Yamaki Mayuko , Sugiura Kazumitsu , Muro Yoshinao , Shimoyama Yoshie , Tomita Yasushi 
Published: June 2010

Please cite this paper as: Epidermal growth factor receptor tyrosine kinase inhibitors induce CCL2 and CCL5 via reduction in IL‐1R2 in keratinocytes. Experimental Dermatology 2010; 19: 730–735.Abstract:  Epidermal growth factor receptor tyrosine kinase (EGFR‐TK) is a transducer of mitogenic signals, and is involved in the pathogenesis and progression of a number of cancers, including non‐small cell lung cancer (NSCLC). Gefitinib is an EGFR‐TK inhibitor that is clinically used to treat NSCLC; however, this drug frequently causes adverse effects, including skin eruptions. The mechanism underlying these skin reactions is elusive, although it is assumed that they are caused by the inhibition of EGFR‐TK signalling in epidermal and adnexal cells. In this article, we demonstrate by immunocytochemistry that the skin lesions of patients treated with oral gefitinib had higher expression of CCL2 and CCL5 compared to normal human epidermis. Further, PD153035, a gefitinib prototype, induced CCL2 and CCL5 mRNA and protein expression in HaCaT and HSC‐1 keratinocyte cell lines with or without interleukin‐1 (IL‐1) treatment in vitro. PD153035 also reduced the levels of interleukin‐1 receptor 2 (IL‐1R2), an IL‐1 decoy receptor. Moreover, we demonstrate that reduction in IL‐1R2 by RNA interference increased IL‐1‐mediated CCL2 and CCL5 mRNA and protein expression. Taken together, our data strongly suggest that IL‐1‐mediated signalling is activated to induce the high expression of CCL2 and CCL5 via reduction in IL‐1R2 in the skin lesions caused by gefitinib.