bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ether lipids and analogs in experimental cancer therapy. A brief review of the munich experience
Authors: Berdel Wolfgang E. 
Published: December 2006

AbstractThis review covers the work of our laboratory on the antineoplastic activity of some ethei lipids and derivatives that are related to platelet‐activating factor (PAF). Various 1‐O‐alkyl lysophospholipid derivatives (ALP) show therapeutic activity in mouse transplant tumor models and in metastatic 3‐Lewis lung carcinoma in vivo. However, certain autochthonous mouse leukemias and radiation‐induced lymphomas are resistant to ALP treatment. The therapeutic effects of these compounds are partially due to the activation of cytotoxic macrophages and direct cytotoxicity.Approximately 20 ether lipids and derivatives were tested for direct cytotoxicity in cells from human solid tumors and leukemias using [3H]thymidine uptake, trypan blue dye exclusion, human tumor clonogenic assays (HTCA) and cell morphology as criteria. Certain ALP, thioether lysophospholipid‐derivatives (TLP), ether0linked lipoidal amines,sn‐2 analogs of PAF, and conjugates of ether lipids and cytosine arabinoside were found cytotoxic in a dose‐ and time‐dependent fashion. Cytotoxicity of some of the ether lipids tested is based on destruction of cell membranes. Structure‐activity studies were performed to better understand the mechanisms leading to accumulation and cytotoxicity of ALP. Comparative studies with normal bone marrow cells and leukemic blasts from humans revealed preferential antileukemic cytotoxity of three ether lipids.
Pregnancy and lactation in a woman with classical galactosaemia heterozygous for p.Q188R and p.R333W
Authors: Ohlsson A. , Nasiell J. , von Döbeln U. 
Published: December 2006

SummaryA 31‐year old patient who is compound heterozygous for the two galactose‐1‐phosphate uridyltransferase mutations p.Q188R and p.R333W delivered two healthy boys after uneventful spontaneous pregnancies. The patient chose to breast‐feed her first baby and her galactose metabolites in blood and urine were monitored closely. A temporary increase in her galactose‐1‐phosphate (gal‐1‐P) levels with a maximum of 0.30 mmol/L on day 2 after delivery was observed. Galactose‐1‐phosphate was normalized 10 days after delivery. At the time of weaning, 8 months after delivery, her menses returned and she had normal sex steroid levels. She became pregnant again 2 months later. The second baby was also breast‐fed. This time an increase in her gal‐1‐P values could be seen for 3 weeks with a maximum gal‐1‐P level of of 0.25 mmol/L at day 7. Only minor changes in her urine galactitol values were noted during the study period but the values stayed in the range of treated galactosaemia patients. We thus report that breast‐feeding has been possible with only small adverse effects on the levels of galactose metabolites in a patient with classical galactosaemia.
Brief report: Sexual sensation seeking and its relationship to risky sexual behaviour among African‐American adolescent females
Authors: Spitalnick Joshua S. , DiClemente Ralph J. , Wingood Gina M. , Crosby Richard A. , Milhausen Robin R. , Sales Jessica M. , McCarty Frances , Rose Eve , Younge Sinead N. 
Published: December 2006

AbstractThe relationship between sexual sensation seeking and sexual risk taking has been investigated among adult populations. There are limited data, however, regarding this relationship for adolescents. Since African‐American adolescent females continue to be disproportionately diagnosed with STDs, including HIV, we examined this association among a clinic‐based sample of African‐American adolescent females (N=715) enrolled in an STD/HIV prevention intervention. Participants (ages 15–21) endorsing higher levels of sexual sensation seeking reported higher levels of sexual risk‐taking behaviours (e.g. frequency of vaginal intercourse, number of sexual partners, and poorer condom use). Results remained significant after controlling for known covariates associated with sexual risk‐taking behaviours. Results are consistent with the adult literature and highlight the need for future investigations examining sexual sensation seeking among adolescents. These results, though preliminary, could be used to better inform prevention interventions and clinicians/health educators who provide direct services to adolescents.
Experimental verification of the acoustic characteristics of the clupeoid diel cycle in the Baltic
Authors: Orlowski Andrzej 
Published: December 2006

Abstract
This paper describes the results of a short-term experiment using measurements of sv from the diel, spatial, clupeoid distribution in the southern Baltic. The aim of the experiment was to verify fish-behaviour characteristics measured over the period from 1995 to 2001. It was also intended to estimate the dynamics of fish behaviour over one separate diel cycle. The studies were based on a 24 h continuous integration of fish echoes using an EY500 echosounder at 38 kHz. Measurements were carried out by RV “Baltica” travelling along the sides of a square of 4 nautical miles at a constant speed of 8 knots. The South Gotland Deep was chosen for the experiment because of the greatest amplitude there of fish vertical, diel migrations within the Polish EEZ. The duration of the experiment was limited by weather conditions, but nearly 300 EDSU samples were collected. 3-D distributions of echoes were correlated to the values of coincident environmental factors of time, depth, water temperature, salinity, and oxygen level. Fish distribution compared with environmental factors is described by different macrosounding visualizations, statistical, and mathematical models. Measurements are compared with the average characteristics of fish behaviour based on data from the autumn acoustic studies between 1995 and 2001 in a wider environment of the Gotland Deep. The results strongly confirmed the instability of the diel acoustic response of fish echoes in both situations. More precise measurements during the experiment indicated the biggest column-scattering strength (Svc) increase during the sunrise period, appearing simultaneously in the whole area. A similar increase was detected by analysis of 1995–2001 data from the South Gotland Deep environment. Major emphasis is given to the explanation of the diel irregularities. Diel instability of fish acoustic response can significantly effect the results of target-strength measurements (up to 400% during the sunrise) and, as a consequence, the calibration of acoustic fish stock-assessment models.
Fish behaviour and orientation-dependent backscatter in acoustic Doppler profiler data
Authors: Zedel Len , Patro Ranjan , Knutsen Tor 
Published: December 2006

Abstract
It is well known that fish target strength can be affected by fish behaviour. In particular, the specific orientation between a target (fish) and an echosounder system is critical in interpreting the apparent target strength. This situation is further complicated for Doppler current-profiler systems that have an array of diverging beams and where each beam will interact with targets with a different orientation. When targets themselves have random orientations, each beam will see the same range of target strengths and the average values would be the same. However, if targets such as schooling fish have a preferred orientation, then an asymmetry is present and different target strengths can be expected. This hypothesis is explored using observations of Norwegian spring-spawning herring (Clupea harengus) under a variety of schooling conditions. When schooling fish are migrating and have well-defined, coherent orientations, differences in backscatter strength of about 5 dB can be seen depending on beam orientation. This difference disappears when fish are not actively migrating and so do not have coherent orientation. These differences can be used to infer behaviour of schooling fish but they also indicate that caution must be exercised when averaging backscatter data from separate Acoustic Doppler Current Profiler (ADCP) beams.
Crystallographic protein model-building on the web
Authors: Gopal Kreshna , McKee Erik , Romo Tod , Pai Reetal , Smith Jacob , Sacchettini James , Ioerger Thomas 
Published: December 2006

AbstractSummary: X-ray crystallography is the most widely used method to determine the 3D structure of protein molecules. One of the most difficult steps in protein crystallography is model-building, which consists of constructing a backbone and then amino acid side chains into an electron density map. Interpretation of electron density maps represents a major bottleneck in protein structure determination pipelines, and thus, automated techniques to interpret maps can greatly improve the throughput. We have developed WebTex, a simple and yet powerful web interface to TEXTAL, a program that automates this process of fitting atoms into electron density maps. TEXTAL can also be downloaded for local installation.Availability: Web interface, downloadable binaries and documentation atContact: textal@tamu.edu
Prophet, a web-based tool for class prediction using microarray data
Authors: Medina Ignacio , Montaner David , Tárraga Joaquín , Dopazo Joaquín 
Published: December 2006

AbstractSample classification and class prediction is the aim of many gene expression studies. We present a web-based application, Prophet, which builds prediction rules and allows using them for further sample classification. Prophet automatically chooses the best classifier, along with the optimal selection of genes, using a strategy that renders unbiased cross-validated errors. Prophet is linked to different microarray data analysis modules, and includes a unique feature: the possibility of performing the functional interpretation of the molecular signature found.Availability: Prophet can be found at the URL or within the GEPAS package atContact: jdopazo@cipf.esSupplementary information:
BioNetBuilder: automatic integration of biological networks
Authors: Avila-Campillo Iliana , Drew Kevin , Lin John , Reiss David J. , Bonneau Richard 
Published: December 2006

AbstractBioNetBuilder is an open-source client-server Cytoscape plugin that offers a user-friendly interface to create biological networks integrated from several databases. Users can create networks for ∼1500 organisms, including common model organisms and human. Currently supported databases include: DIP, BIND, Prolinks, KEGG, HPRD, The BioGrid and GO, among others. The BioNetBuilder plugin client is available as a Java Webstart, providing a platform-independent network interface to these public databases.Availability: Contact: iliana_avila-campillo@merck.com
K-Fold: a tool for the prediction of the protein folding kinetic order and rate
Authors: Capriotti E. , Casadio R. 
Published: December 2006

AbstractSummary: K-Fold is a tool for the automatic prediction of the protein folding kinetic order and rate. The tool is based on a support vector machine (SVM) that was trained on a data set of 63 proteins, whose 3D structure and folding mechanism are known from experiments already described in the literature. The method predicts whether a protein of known atomic structure folds according to a two-state or a multi-state kinetics and correctly classifies 81% of the folding mechanisms when tested over the training set of the 63 proteins. It also predicts as a further option the logarithm of the folding rate. To the best of our knowledge, the tool discriminates for the first time whether a protein is characterized by a two state or a multiple state kinetics, during the folding process, and concomitantly estimates also the value of the constant rate of the process. When used to predict the logarithm of the folding rate, K-Fold scores with a correlation value to the experimental data of 0.74 (with a SE of 1.2).Availability: Contact: emidio@biocomp.unibo.itSupplementary information:
Flexible empirical Bayes models for differential gene expression
Authors: Lo Kenneth , Gottardo Raphael 
Published: December 2006

AbstractMotivation: Inference about differential expression is a typical objective when analyzing gene expression data. Recently, Bayesian hierarchical models have become increasingly popular for this type of problem. The two most common hierarchical models are the hierarchical Gamma–Gamma (GG) and Lognormal–Normal (LNN) models. However, to facilitate inference, some unrealistic assumptions have been made. One such assumption is that of a common coefficient of variation across genes, which can adversely affect the resulting inference.Results: In this paper, we extend both the GG and LNN modeling frameworks to allow for gene-specific variances and propose EM based algorithms for parameter estimation. The proposed methodology is evaluated on three experimental datasets: one cDNA microarray experiment and two Affymetrix spike-in experiments. The two extended models significantly reduce the false positive rate while keeping a high sensitivity when compared to the originals. Finally, using a simulation study we show that the new frameworks are also more robust to model misspecification.Availability: The R code for implementing the proposed methodology can be downloaded atContact: c.lo@stat.ubc.caSupplementary information: The supplementary material is available at
Freeze-Thaw Lysis for Extraction of Proteins from Mammalian Cells
Authors: Tansey William P. 
Published: December 2006

INTRODUCTIONThis protocol describes the extraction of proteins from mammalian cells grown in 6- or 10-cm tissue-culture dishes. It is useful for making very concentrated extracts for Western blotting, and is particularly helpful when low-abundance proteins such as Myc are being studied.
Detection of Ubiquitylated Proteins in Yeast
Authors: Tansey William P. 
Published: December 2006

INTRODUCTIONThis assay is performed to detect ubiquitylated proteins in yeast. Yeast that have been transformed with a vector expressing polyhistidine-tagged ubiquitin (Ub) under the control of a copper-inducible promoter are grown, induced with copper, and harvested. Total ubiquitylated proteins are then recovered by nickel-affinity chromatography, and specific proteins are detected by Western blotting.
Constructing and Expressing GFP Fusion Proteins
Authors: Spector David L. , Goldman Robert D. 
Published: December 2006

INTRODUCTIONGFP (green fluorescent protein) fusion proteins have been used to address a wide range of questions in individual cells, as well as in tissues of a particular organism. GFP fusion proteins can be transiently or stably expressed. Although transient expression is quick and can provide informative results, in many cases it is beneficial and/or essential to develop stable cell lines expressing the fusion protein of interest. In addition to providing more native levels of expression, individual clones can be generated from single cells, the integration site of the plasmid mapped, and the copy number determined. Because every cell in the population is expressing the fusion protein, cell cycle analyses and biochemical fractionation are significantly easier to accomplish. The following protocol can be used for the development of stable cell lines expressing GFP fusion proteins. Although optimal transfection procedures (e.g., calcium phosphate, electroporation, or FuGENE 6 [Roche Applied Science]) vary depending on cell type, this general transfection procedure has been successful for stable transfection of HeLa, A-431, U2OS, BHK, and HT1080 cells.
Gene Delivery by Direct Injection (Microinjection) Using a Controlled-Flow System
Authors: Dean David A. 
Published: December 2006

INTRODUCTIONThis protocol describes a method for constant-flow microinjection using the Pneumatic PicoPump (World Precision Instruments). This type of system is very simple and can be assembled on a relatively low budget. In this method, a constant flow of sample is delivered from the tip of the pipette, and the amount of sample injected into the cell is determined by how long the pipette remains in the cell. A typical system is composed of a pressure regulator that can be adjusted for two pressures (back pressure and injection pressure), a capillary holder, and a coarse and fine micromanipulator.
Silver Staining, Digestion, and Extraction of Peptides from an Acrylamide Gel for MS Analysis
Authors: Niessen Sherry , Mcleod Ian , Yates John R. 
Published: December 2006

INTRODUCTIONIndividual components of protein complexes separated by sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE) are visualized by silver (or Coomassie) staining. For subsequent analysis by mass spectrometry (MS), it is important to use silver staining protocols with no glutaraldehyde, as this reagent chemically modifies the protein and inhibits subsequent steps. The individual stained protein bands are excised from the gel, the proteins are enzymatically digested into peptides, and the peptides are extracted. The peptides from each protein can be subsequently analyzed by high-pressure liquid chromatography (HPLC) fractionation and electrospray ionization (ESI) MS. This generates a mass fingerprint of the peptides that comprise the unknown protein. Further structural data for peptides can be obtained by fragmenting the ionized peptides to generate a tandem mass spectrum. Alternatively, a mass fingerprint of the peptides is obtained by matrix-assisted laser desorption/ionization in combination with a time-of-flight instrument (MALDI/TOF).
Direct Enzymatic Digestion of Protein Complexes for MS Analysis
Authors: Niessen Sherry , Mcleod Ian , Yates John R. 
Published: December 2006

INTRODUCTIONThe individual components of a purified protein complex can be determined by MS. Components can be separated by SDS-PAGE and subsequently digested, or the entire protein complex can be digested by chemical agents or by proteases. The mixture of peptides that results from digestion without prior separation is more complex than that obtained from the digestion of a single protein, and can best be resolved subsequently using HPLC in combination with a biphasic column. Protein complexes can be digested directly using several different protocols. Common methods include a double digest with endoproteinase Lys-C and trypsin, or a triple digest with elastase, subtilisin, and trypsin. Endoproteinase Lys-C cleaves carboxy-terminal to lysine residues, while trypsin cleaves carboxy-terminal to lysine and arginine residues. The triple digest uses the relatively nonspecific proteases elastase and subtilisin to create a large number of overlapping peptides for the analysis of post-translational modifications. The double and triple digest protocols begin with the reduction and alkylation of cysteine residues to disrupt disulfide bonds and, therefore, higher-order protein structure.
HPLC Separation of Digested Proteins and Preparation for Matrix-Assisted Laser Desorption/Ionization Analysis
Authors: Niessen Sherry , Mcleod Ian , Yates John R. 
Published: December 2006

INTRODUCTIONTwo types of columns are commonly used for the separation of peptides by HPLC. A single-phase column contains the reverse-phase resin C18, which interacts with the hydrophobic moieties of the peptides. Peptides resulting from digestion of simple mixtures of proteins are loaded onto the single-phase column and eluted into the mass analyzer using an increasing gradient of an organic solvent. Peptides resulting from the digestion of more complex mixtures of proteins are resolved using a biphasic column. This column integrates both a strong cation exchange SCX resin, which interacts with peptides as a result of their positive charge, and a reverse-phase C18 resin, packed in tandem. Peptides initially interact with the SCX resin and are eluted into the C18 resin by ammonium acetate that competes for the peptide-binding sites. Peptides are then eluted from the C18 resin into the mass analyzer. This process is repeated using increasing concentrations of ammonium acetate to differentially elute peptides in a stepwise fashion. The biphasic column also uses an additional C18 reverse-phase resin linked through an Inline MicroFilter Assembly (Upchurch) to desalt the peptides prior to loading onto the SCX. The desalting and biphasic columns are combined to give an integrated desalting/biphasic column.
Transformation of Agrobacterium Using the Freeze-Thaw Method
Authors: Weigel Detlef , Glazebrook Jane 
Published: December 2006

INTRODUCTIONThis protocol describes a method for transforming Agrobacterium with plasmid DNA using a freeze-thaw technique. Although the transformation efficiency for Agrobacterium is lower than that for Escherichia coli, it is possible to obtain adequate numbers of transformants with this technique.
In Planta Transformation of Arabidopsis
Authors: Weigel Detlef , Glazebrook Jane 
Published: December 2006

INTRODUCTIONA breakthrough in Arabidopsis research was the invention of the vacuum-infiltration procedure, a simple and reliable method of obtaining transformants at high efficiency while avoiding the use of tissue culture. The plant transformation procedures described here involve floral dip, vacuum infiltration, and spraying. They yield transformants at frequencies ranging up to several percent, with the most common frequency being 0.1%-1%.
Kanamycin Selection of Transformed Arabidopsis
Authors: Weigel Detlef , Glazebrook Jane 
Published: December 2006

INTRODUCTIONThe most commonly used markers for selection of transgenic Arabidopsis are resistance to the antibiotic kanamycin and to the herbicide glufosinate ammonium. Resistance to kanamycin is conferred by a bacterial gene encoding the enzyme neomycin phosphotransferase (NPT). In this protocol, kanamycin-resistant seedlings are selected on solid medium.
Glufosinate Ammonium Selection of Transformed Arabidopsis
Authors: Weigel Detlef , Glazebrook Jane 
Published: December 2006

INTRODUCTIONOne of the most commonly used markers for the selection of transgenic Arabidopsis is resistance to glufosinate ammonium, an herbicide that is sold under a variety of trade names including Basta and Finale. Resistance to glufosinate ammonium is conferred by the bacterial bialophos resistance gene (BAR) encoding the enzyme phosphinotricin acetyl transferase (PAT). This protocol describes the use of glufosinate ammonium to select transformed Arabidopsis plants. The major advantage of glufosinate ammonium selection is that it can be performed on plants growing in soil and does not require the use of sterile techniques.