bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oily Grime Formed on Hard Surfaces of Kitchen Appliances: (Part 2) Kinetics of Oily Grime Removal
Authors: Yamada Kaoru , Tsutsui Takuya , Natsuhara Masahiko , Tanizawa Yoshiaki 
Published: June 2007

AbstractThe oily grime adsorbed to the surfaces of kitchen appliances ages to become difficult to remove using normal dishwashing detergents. Artificial grime models similar to actual grime were prepared using composition data of the oily grime obtained in previous work. To evaluate typical cleaning products, one needs to observe their efficacy against actual and artificial grime using precise and objective evaluation methods. In the present work, the kinetic method was applied to actual kitchen grime. The grime‐removal rate constants were calculated by monitoring absorbance of the cleaning fluids, and the results are discussed based on the compositions of the detergents and grime. One commercial detergent, with pH adjusted to 9.7, consisted mainly of spirit solvent and had two rate constants, k1 (fast) and k2 (slow), which indicated the removal rates of THF‐soluble and THF‐insoluble oily grime, respectively. With a second commercial detergent that contained mainly an alkali agent at pH 11.8, the removal rates were extremely fast for both THF‐soluble and THF‐insoluble grime. The alkalinity worked effectively against both types of grime. The effects on the removal rates of various ingredients that could be added to the cleaning products were also investigated and the overall removal rates were highly dependent on the pH of the fluids and slightly dependent on the kinds of alkalies used. The present kinetic method was found to be useful for evaluating the capability of the detergents. The plural rate constants observed for a single grime sample, which previously were not well understood, could be interpreted in terms of the compositions of the grime.
Dietary Lipids Impacts on Healthy Ageing
Authors: Okuyama Harumi , Yamada Kazuyo , Miyazawa Daisuke , Yasui Yuko , Ohara Naoki 
Published: June 2007

AbstractHealthy ageing is gaining attention in the lipid nutrition field. As in vivo biomarkers of healthy ageing, we have evaluated the survival, learning/memory performance, and physical potencies in rodents fed a diet supplemented with high‐linoleic acid (LNA, ω6) safflower oil or high‐α‐linolenic acid (ALA, ω3) perilla oil for long periods. The results suggested that perilla oil with a low ω6/ω3 ratio is beneficial for healthy ageing. In order to address this issue further, we determined the survival of stroke‐prone SHR (SHRSP) rats fed a conventional rodent diet supplemented with 10% fat or oil. Survival was longer with ω3‐rich oils compared with ω6‐rich oils. However, some kinds of vegetable oils and hydrogenated oils shortened the survival of SHRSP rats to an unusual degree (ca. 40% compared with that of ω6‐rich oil) that could not be accounted for by the fatty acid and phytosterol composition of the oils. The observed decrease in platelet counts was associated with pathological changes in the kidney and other organs. Dihydro‐vitamin K1 is proposed as a likely candidate as a stroke‐stimulating factor in hydrogenated oils. Thus, factors other than fatty acids (ω6/ω3 balance) and phytosterols must be taken into account when fats and oils are evaluated in relation to healthy ageing.
Acute elevation of plasma non-esterified fatty acids increases pulse wave velocity and induces peripheral vasodilation in humansin vivo
Authors: Riksen Niels P. , Bosselaar Marlies , Bakker Stephan J.L. , Heine Robert J. , Rongen Gerard A. , Tack Cees J. , Smits Paul 
Published: June 2007

Plasma NEFA (non-esterified fatty acid) concentrations are elevated in patients with obesity. In the present study we first aimed to provide an integral haemodynamic profile of elevated plasma NEFAs by the simultaneous assessment of blood pressure, pulse wave velocity, FBF (forearm blood flow) and sympathetic nervous system activity during acute elevation of NEFAs. Secondly, we hypothesized that NEFA-induced vasodilation is mediated by adenosine receptor stimulation. In a randomized cross-over trial in healthy subjects, Intralipid® was infused for 2 h to elevate plasma NEFAs. Glycerol was administered as the Control infusion. We assessed blood pressure, pulse wave velocity, FBF (using venous occlusion plethysmography) and sympathetic nervous system activity by measurement of noradrenaline and adrenaline. During the last 15 min of Intralipid®/Control infusion, the adenosine receptor antagonist caffeine (90 μg·min−1·dl−1) was administered into the brachial artery of the non-dominant arm. Compared with Control infusion, Intralipid® increased pulse wave velocity, SBP (systolic blood pressure) and pulse pressure, as well as FBF (from 1.8±0.2 to 2.7±0.6 and from 2.3±0.2 to 2.7±0.6 ml·min−1·dl−1 for Intralipid® compared with Control infusion; P&lt;0.05, n=9). Although in a positive control study caffeine attenuated adenosine-induced forearm vasodilation (P&lt;0.01, n=6), caffeine had no effect on Intralipid®-induced vasodilation (P=0.5). In conclusion, elevation of plasma NEFA levels increased pulse wave velocity, SBP and pulse pressure. FBF was also increased, either by baroreflex-mediated inhibition of the sympathetic nervous system or by a direct vasodilating effect of NEFAs. As the adenosine receptor antagonist caffeine could not antagonize the vasodilator response, this response is not mediated by adenosine receptor stimulation.
Simple and fast alignment of metabolic pathways by exploiting local diversity
Authors: Wernicke Sebastian , Rasche Florian 
Published: June 2007

AbstractMotivation: An important tool for analyzing biological networks is the ability to perform homology searches, i.e. given a pattern network one would like to be able to search for occurrences of similar (sub)networks within a set of host networks. In the context of metabolic pathways, Pinter et al. [Bioinformatics, 2005] proposed to solve this computationally hard problem by restricting it to the case where both the pattern and host networks are trees. This restriction, however, severely limits the applicability of their algorithm.Results: We propose a very fast and simple algorithm for the alignment of metabolic pathways that does not restrict the topology of the host or pattern network in any way; instead, our algorithm exploits a natural property of metabolic networks that we call ‘local diversity property’. Experiments on a test bed of metabolic pathways from the BioCyc database indicate that our algorithm is much faster than the restricted algorithm of Pinter et al.—the metabolic pathways of two organisms can be aligned in mere seconds—and yet has a wider range of applicability and yields new biological insights. Our ideas can likely be extended to work for the alignment of various types of biological networks other than metabolic pathways.Availability: Our algorithm has been implemented in C++ as a user-friendly metabolic pathway alignment tool called METAPAT. The tool runs under Linux or Windows and can be downloaded at http://theinf1.informatik.uni-jena.de/metapat/;Contact: florian.rasche@uni-jena.deSupplementary information: Supplementary data are available at bioinformatics online.
VISDA: an open-source caBIG™ analytical tool for data clustering and beyond
Authors: Wang Jiajing , Li Huai , Zhu Yitan , Yousef Malik , Nebozhyn Michael , Showe Michael , Showe Louise , Xuan Jianhua , Clarke Robert , Wang Yue 
Published: June 2007

AbstractSummary: VISDA (Visual Statistical Data Analyzer) is a caBIG™ analytical tool for cluster modeling, visualization and discovery that has met silver-level compatibility under the caBIG initiative. Being statistically principled and visually interfaced, VISDA exploits both hierarchical statistics modeling and human gift for pattern recognition to allow a progressive yet interactive discovery of hidden clusters within high dimensional and complex biomedical datasets. The distinctive features of VISDA are particularly useful for users across the cancer research and broader research communities to analyze complex biological data.Availability: http://gforge.nci.nih.gov/projects/visda/Contact: yuewang@vt.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Dissociation and Reaggregation of Xenopus laevis Animal Caps
Authors: Sive Hazel L. , Grainger Robert M. , Harland Richard M. 
Published: June 2007

INTRODUCTIONPreparations of single cells from Xenopus laevis animal caps are useful for assaying the activity of inducing molecules. These dissociated cells can be exposed to more uniform concentrations of inducing factors than the multilayered intact cap. Single cells derived from caps are also used to analyze the role of cell-to-cell contact. This protocol describes the preparation of cells from Xenopus for use in such assays. Animal caps require divalent cations for their integrity and thus can be dissociated by exposure to medium lacking Ca++ and Mg++ ions. With this treatment, the cells comprising the inner layers of the cap dissociate within ~20 minutes. Cells can be reaggregated after this treatment and should survive well. The outer layer of cells is more recalcitrant to dissociation and requires a more severe treatment.
Ectodermal (Animal Cap) Layer Separations in Xenopus laevis: Figure 1.
Authors: Sive Hazel L. , Grainger Robert M. , Harland Richard M. 
Published: June 2007

INTRODUCTIONIn Xenopus laevis, the blastula animal cap comprises two morphologically distinct cell layers, an outer monolayer termed the epithelial layer, which consists of tightly adherent pigmented cells, and an inner layer several cells thick termed the sensorial layer, which consists of loosely adherent cells. It is possible to isolate cell layers and to test their developmental potential and response to induction. This protocol describes how to separate the cell layers most easily, that is, by dissecting an intact Xenopus embryo.
Xenopus laevis Einstecks
Authors: Sive Hazel L. , Grainger Robert M. , Harland Richard M. 
Published: June 2007

INTRODUCTION“Einstecks” refers to a procedure for placing a piece of tissue into the blastocoel of an early gastrula, in order to assess the inductive potential of the introduced tissue. The foreign tissue adheres to surrounding tissue and becomes incorporated into the host embryo. This simple transplant procedure, which is described here, has been used to assess which types of axial tissue can be induced by different regions of the mesendoderm or ectoderm, and how forced expression of genes or treatment with various factors can alter this potential.
Transplantation of Xenopus laevis Lens Ectoderm
Authors: Sive Hazel L. , Grainger Robert M. , Harland Richard M. 
Published: June 2007

INTRODUCTIONIn Xenopus laevis, transplanting a piece of tissue from one site to another (other than into the blastocoel) is a useful way of examining the sequence of inductions required to produce a particular organ. For example, the young primordium of a particular organ can be transplanted from a young individual into an older embryo to determine whether the older embryo still has the capacity to induce the tissue to form the organ. Although this capacity can also be assayed using explants, the complex surroundings of the host embryo cannot be reproduced in an explant. This protocol describes how to transplant a piece of gastrula-stage animal cap ectoderm into the presumptive lens of a neural-plate-stage host embryo. Note that the technique can be adapted for use in other regions of the embryo. Care must be taken to inflict as little damage on the embryo as possible during this procedure. Well-treated embryos recover rapidly, whereas embryos with extensive injuries do not.
Cortical Isolation from Xenopus laevis Oocytes and Eggs: Figure 1.
Authors: Sive Hazel L. , Grainger Robert M. , Harland Richard M. 
Published: June 2007

INTRODUCTIONIn Xenopus laevis, the cortex is the layer of gelatinous cytoplasm that lies just below the plasma membrane of the egg. Rotation of the cortex relative to the deeper cytoplasm soon after fertilization is intimately linked to normal dorsal axis specification. The cortex can be dissected from the egg to analyze its composition and activity or to clone associated RNAs. This protocol describes a procedure for isolating the vegetal cortex of the fertilized egg.
An Approach for Immunofluorescence of Drosophila S2 Cells: Figure 1.
Authors: Angshuman Sarkar , Cordula Schulz 
Published: June 2007

INTRODUCTIONImmunofluorescence is widely used as a technique for visualization of a specific protein in cells or tissue sections. The two major types of immunofluorescence staining methods are (1) direct immunofluorescence staining, in which the primary antibody is labeled with fluorescence dye, and (2) indirect immunofluorescence staining, in which a secondary antibody labeled with fluorochrome is used to recognize a primary antibody. Immunofluorescence staining can be performed on whole tissue, tissue sections, or cells fixed on slides. Despite the availability of various immunofluorescence protocols, it is still a challenge to work with Drosophila S2 cells because of their poor attachment and comparatively low permeability. Here we provide a modified and standardized immunofluorescence protocol specifically for S2 cells.
RNA FISH on Cultured Cells in Interphase: Figure 1.
Authors: Karen Ng , Wutz Anton 
Published: June 2007

INTRODUCTIONFluorescence in situ hybridization (FISH) has become a widely used method in genome and molecular genetic studies. The technique is highly versatile and has been adapted to carry out genome-wide screenings, microarray quantifications, cancer cytogenetics analysis, and RNA expression and localization studies. The study of intracellular RNA localization using RNA FISH provides insights into the in situ physical characteristics of transcription and intracellular RNA transport in individual cells. In our lab, we use RNA FISH to detect the localization of Xist RNA, a nuclear noncoding transcript that coats the entire chromosome from which it is transcribed. The advantage of using RNA FISH in our case is to extract precise molecular information directly in the context of cellular structure. The RNA FISH technique requires the generation of a labeled probe, hybridization of the probe to a fixed sample, and detection of the labeled probe using microscopy.
A Solid-Phase Immunostaining Protocol for High-Resolution Imaging of Delicate Structures in the Drosophila Larval Central Nervous System (CNS)
Authors: Daubert Elizabeth A. , Condron Barry G. 
Published: June 2007

INTRODUCTIONThis protocol describes a method for mounting and immunostaining Drosophila larval tissue in preparation for high-resolution fluorescent imaging of fine structures in the central nervous system (CNS). Affixing the tissue directly to the coverslip and then moving the coverslip between wash solutions provides a simple solid-phase method of immunostaining that assists in preserving fine structures. This method also easily allows for manipulations and/or viewing of the live sample prior to fixation if desired. Finally, putting the tissue in direct contact with the coverslip places fine structures immediately adjacent to the objective lens. We also briefly describe a method to create three-dimensional (3D) models of confocal Z-stacks in order to better characterize fine structures by measuring their volume and obtaining 3D Cartesian coordinates in space.
Preparation of Zebrafish Embryos for Transmission Electron Microscopy
Authors: Rieger Sandra , Köster Reinhard W. 
Published: June 2007

INTRODUCTIONThis protocol describes a procedure for the fixation and embedding of zebrafish embryos at organogenesis stages (48-72 hours post-fertilization [hpf]) for transmission electron microscopy (TEM). The lengths of individual steps may be adjusted according to the developmental stage of the specimen.
Expression of androgen receptor and two androgen‐induced proteins (apolipoprotein D and pepsinogen C) in ductal carcinoma in situ of the breast
Authors: Gonzalez L O , Corte M D , Junquera S , Bongera M , Rodriguez J C , Vizoso F J 
Published: June 2007

Aims:  To evaluate the expression of androgen receptors (AR) and two androgen‐induced proteins [apolipoprotein D (ApoD) and pepsinogen C (PepC)] in ductal carcinoma in situ (DCIS) of the breast.Methods and results:  AR, ApoD and PepC expression was examined in 28 cases of pure DCIS and in 31 cases of DCIS adjacent to invasive carcinoma of the breast using immunohistochemical methods and then correlated with the architectural subtype, the degree of differentiation and the ostrogen receptor (ER)/progesterone receptor (PgR)/HER‐2 status. We found no significant differences between pure DCIS and DCIS adjacent to invasive breast cancer regarding the percentage of positive cases for ApoD (64.3% versus 54.8%), PepC (42.9% versus 48.4%), ER (64.3% versus 58.1%), PgR (60.7% versus 58.1%) and HER‐2 (39.3% versus 67.7%). However, there was a significantly higher percentage of AR+ DCIS among those adjacent to invasive carcinomas of the breast than among pure DCIS lesions (93.5% versus 60.9%) (P = 0.009). AR expression did not correlate with architectural subtype, degree of differentiation, or ER/PgR/HER‐2/ApoD/PepC status, in cases of pure DCIS, nor in DCIS adjacent to invasive carcinoma of the breast.Conclusions:  AR expression may represent an independent predictive factor in DCIS of the breast.
Detection of the ASPSCR1–TFE3 gene fusion in paraffin‐embedded alveolar soft part sarcomas
Authors: Aulmann S , Longerich T , Schirmacher P , Mechtersheimer G , Penzel R 
Published: June 2007

Aims:  Alveolar soft part sarcoma (ASPS) is a rare soft tissue tumour with unique morphology and a recurrent, non‐reciprocal translocation der(17)t(X;17)(p11.2;q25) leading to the fusion of ASPSCR1 (also known as ASPL) to the transcription factor TFE3. Although diagnosis is straightforward in classical cases, tumours with atypical morphological features may be difficult to classify solely on the basis of conventional histopathology. The aim of this study was to analyse the chromosomal breakpoints in paraffin‐embedded tissue.Methods and results:  Three male and two female ASPS patients including one case with uncommon histology were investigated by fluorescence in situ hybridization with split‐ and fusion‐probes. The presence of the resulting ASPSCR1–TFE3 fusion transcripts was assessed by reverse transcriptase‐polymerase chain reaction. Hybridization results showed a t(X;17)(p11.2;q25) in all tumours with a duplication of the telomeric part of chromosome Xp. In addition to wild‐type TFE3, ASPSCR1–TFE3 fusion transcripts (three type 1 and two type 2 transcripts) were detected in all cases.Conclusions:  Molecular confirmation of ASPSCR1–TFE3 gene fusion is applicable to routinely processed archival and diagnostic tumour samples and aids in the differential diagnosis of ASPS.
Chromatin assembly factor‐1 (CAF‐1)‐mediated regulation of cell proliferation and DNA repair: a link with the biological behaviour of squamous cell carcinoma of the tongue?
Authors: Staibano S , Mignogna C , Lo Muzio L , Mascolo M , Salvatore G , Di Benedetto M , Califano L , Rubini C , De Rosa G 
Published: June 2007

Aims:  Squamous cell carcinoma (SCC) of the tongue shows aggressive behaviour and a poor prognosis. Clinicopathological parameters fail to provide reliable prognostic information, so the search continues for new molecular markers for this tumour. Chromatin assembly factor‐1 (CAF‐1) plays a major role in chromatin assembly during cell replication and DNA repair and has been proposed as a new proliferation marker. The aim of this study was to investigate its expression in SCC of the tongue.Methods and results:  The immunohistochemical expression of the p60 and p150 subunits of CAF‐1 were evaluated in a series of SCCs of the tongue. The findings were correlated with the expression of proliferation cell nuclear antigen (PCNA) and patients' clinicopathological and follow‐up data. CAF‐1/p60 was expressed in all the tumours, whereas CAF‐1/p150 was down‐regulated in a number of cases. Overexpression of CAF‐1/p60 and down‐regulation of CAF‐1/p150 identified SCCs with poor outcome, in addition to the classical prognostic parameters.Conclusions:  Simultaneous CAF‐1‐mediated deregulation of cell proliferation and DNA repair takes place in aggressive SCC of the tongue. Therefore, the evaluation of CAF‐1 expression may be a valuable tool for evaluation of the biological behaviour of these tumours. This may be relevant to the introduction of improved follow‐up protocols and/or alternative therapeutic regimens.
Heritability of diurnal type: a nationwide study of 8753 adult twin pairs
Authors: KOSKENVUO MARKKU , HUBLIN CHRISTER , PARTINEN MARKKU , HEIKKILÄ KAUKO , KAPRIO JAAKKO 
Published: June 2007

SummaryTwin studies suggest a genetic component in diurnal types. In 1981, a questionnaire sent to the Older Finnish Twin Cohort yielded responses from 2836 adult monozygotic (MZ) and 5917 like‐sexed dizygotic (DZ) twin pairs with four category self‐report on diurnal type. We used structural equation modelling to estimate genetic and environmental components of variance in morningness and eveningness. The model fitting was best when the morningness and the eveningness were analysed together. The ADE‐model (including additive genetic, dominant genetic and non‐shared environmental effects) fitted best to the data. ADE‐models for men and women separately did not differ in a statistically significant manner from the combined model, and similarly ADE‐models for young and old age groups separately did not differ either. The estimate for overall genetic effect (broad sense heritability) was 49.7% (95% confidence interval 46.4–52.8), with the remainder accounted for by environmental factors not shared by siblings. The variance component estimates for the underlying liability to diurnal type were 11.7% (95% CI 0–23.7) for additive genetic factors, 38.0% (24.7–51.3) for genetic factors due to dominance. Genetic effects thus account for about one‐half of the interindividual variability in diurnal type in adults.
Robust circadian rhythm in heart rate and its variability: influence of exogenous melatonin and photoperiod
Authors: VANDEWALLE GILLES , MIDDLETON BENITA , RAJARATNAM SHANTHA M. W. , STONE BARBARA M. , THORLEIFSDOTTIR BJORG , ARENDT JOSEPHINE , DIJK DERK‐JAN 
Published: June 2007

SummaryHeart rate (HR) and heart rate variability (HRV) undergo marked fluctuations over the 24‐h day. Although controversial, this 24‐h rhythm is thought to be driven by the sleep–wake/rest–activity cycle as well as by endogenous circadian rhythmicity. We quantified the endogenous circadian rhythm of HR and HRV and investigated whether this rhythm can be shifted by repeated melatonin administration while exposed to an altered photoperiod. Eight healthy males (age 24.4 ± 4.4 years) participated in a double‐blind cross‐over design study. In both conditions, volunteers were scheduled to 16 h–8 h rest : wake and dark : light cycles for nine consecutive days preceded and followed by 29‐h constant routines (CR) for assessment of endogenous circadian rhythmicity. Melatonin (1.5 mg) or placebo was administered at the beginning of the extended sleep opportunities. For all polysomnographically verified wakefulness periods of the CR, we calculated the high‐ (HF) and low‐ (LF) frequency bands of the power spectrum of the R–R interval, the standard deviation of the normal‐to‐normal (NN) intervals (SDNN) and the square root of the mean‐squared difference of successive NN intervals (rMSSD). HR and HRV variables revealed robust endogenous circadian rhythms with fitted maxima, respectively, in the afternoon (16:36 hours) and in the early morning (between 05:00 and 06:59 hours). Melatonin treatment phase‐advanced HR, HF, SDNN and rMSSD, and these shifts were significantly greater than after placebo treatment. We conclude that endogenous circadian rhythmicity influences autonomic control of HR and that the timing of these endogenous rhythms can be altered by extended sleep/rest episodes and associated changes in photoperiod as well as by melatonin treatment.