Fully automated software solution for protein quantitation by global metabolic labeling with stable isotopes

Metabolic stable isotope labeling is increasingly employed for accurate protein (and metabolite) quantitation using mass spectrometry (MS). It provides sample-specific isotopologues that can be used to facilitate comparative analysis of two or more samples. Stable Isotope Labeling by Amino acids in Cell culture (SILAC) has been used for almost a decade in proteomic research and analytical software solutions have been established that provide an easy and integrated workflow for elucidating sample abundance ratios for most MS data formats. While SILAC is a discrete labeling method using specific amino acids, global metabolic stable isotope labeling using isotopes such as (15)N labels the entire element content of the sample, i.e. for (15)N the entire peptide backbone in addition to all nitrogen-containing side chains. Although global metabolic labeling can deliver advantages with regard to isotope incorporation and costs, the requirements for data analysis are more demanding because, for instance for polypeptides, the mass difference introduced by the label depends on the amino acid composition. Consequently, there has been less progress on the automation of the data processing and mining steps for this type of protein quantitation. Here, we present a new integrated software solution for the quantitative analysis of protein expression in differential samples and show the benefits of high-resolution MS data in quantitative proteomic analyses.

Eco-labeling, rents, sales prices and occupancy rates: do LEED and Energy Star labeled offices obtain multiple premiums?

Drawing upon an updated and expanded dataset of Energy Star and LEED labeled commercial offices, this paper investigates the effect of eco-labeling on rental rates, sale prices and occupancy rates. Using OLS and robust regression procedures, hedonic modeling is used to test whether the presence of an eco-label has a significant positive effect on rental rates, sale prices and occupancy rates. The study suggests that estimated coefficients can be sensitive to outlier treatment. For sale prices and occupancy rates, there are notable differences between estimated coefficients for OLS and robust regressions. The results suggest that both Energy Star and LEED offices obtain rental premiums of approximately 3%. A 17% sale price premium is estimated for Energy Star labeled offices but no significant sale price premium is estimated for LEED labeled offices. Surprisingly, no significant occupancy premium is estimated for Energy Star labeled offices and a negative occupancy premium is estimated for LEED labeled offices.

An investigation of the effect of eco-labeling on office occupancy rates

This paper investigates the extent to which clients were able to influence performance measurement appraisals during the downturn in commercial property markets that began in the UK during the second half of 2007. The sharp change in market sentiment produced speculation that different client categories were attempting to influence their appraisers in different ways. In particular, it was recognised that the requirement for open-ended funds to meet redemptions gave them strong incentives to ensure that their asset values were marked down to market. Using data supplied by Investment Property Databank, we demonstrate that, indeed, unlisted open ended funds experienced sharper drops in capital values than other fund types in the second half of 2007, after the market turning point. These differences are statistically significant and cannot simply be explained by differences in portfolio composition. Client influence on appraisal forms one possible explanation of the results observed: the different pressures on fund managers resulting in different appraisal outcomes.

Updated empirical model of genetically-modified maize grain production practices to achieve European Union labeling thresholds

An updated empirical approach is proposed for specifying coexistence requirements for genetically modified (GM) maize (Zea mays L.) production to ensure compliance with the 0.9% labeling threshold for food and feed in the European Union. The model improves on a previously published (Gustafson et al., 2006) empirical model by adding recent data sources to supplement the original database and including the following additional cases: (i) more than one GM maize source field adjacent to the conventional or organic field, (ii) the possibility of so-called “stacked” varieties with more than one GM trait, and (iii) lower pollen shed in the non-GM receptor field. These additional factors lead to the possibility for somewhat wider combinations of isolation distance and border rows than required in the original version of the empirical model. For instance, in the very conservative case of a 1-ha square non-GM maize field surrounded on all four sides by homozygous GM maize with 12 m isolation (the effective isolation distance for a single GM field), non-GM border rows of 12 m are required to be 95% confident of gene flow less than 0.9% in the non-GM field (with adventitious presence of 0.3%). Stacked traits of higher GM mass fraction and receptor fields of lower pollen shed would require a greater number of border rows to comply with the 0.9% threshold, and an updated extension to the model is provided to quantify these effects.

The use of fluorescein for labeling genomic probes in the checkerboard DNA-DNA hybridization method

Molecular methods that permit the simultaneous detection and quantification of a large number of microbial species are currently employed in the evaluation of complex ecosystems. The checkerboard DNA-DNA hybridization technique enables the simultaneous identification of distinct bacterial. species in a large number of dental samples. The original technique employed digoxigenin-labeled whole genomic DNA probes which were detected by chemiluminescence. In this study, we present an alternative protocol for labeling and detecting whole genomic DNA probes in the Checkerboard DNA-DNA hybridization method. Whole genomic DNA was extracted from five bacterial species and labeled with fluorescein. The fluorescein labeled whole genomic DNA probes were hybridized against whole genomic DNA or subgingival plaque samples in a checkerboard hybridization format, followed by chemiluminescent detection. Our results reveal that fluorescein is a viable and adequate alternative labeling reagent to be employed in the checkerboard DNA-DNA hybridization technique. (c) 2007 Elsevier GmbH. All rights reserved.

Microbiological Shelf Life of Pasteurized Milk in Bottle and Pouch

Shelf life of pasteurized milk in Brazil ranges from 3 to 8 d, mainly due to poor cold chain conditions that prevail throughout the country and subject the product to repeated and/or severe temperature abuse. This study evaluated the influence of storage temperature on the microbiological stability of homogenized whole pasteurized milk (75 degrees C/15 s) packaged in high-density polyethylene (HDPE) bottle and low-density polyethylene (LDPE) pouch, both monolayer materials pigmented with titanium dioxide (TiO(2)). The storage temperatures investigated were 2, 4, 9, 14, and 16 degrees C. Microbiological evaluation was based on mesophilic and psychrotrophic counts with 7 log CFU/mL and 6 log CFU/mL, respectively, set as upper limits of acceptability for maintaining the quality of milk. The microbiological stability for pasteurized milk packaged in HDPE bottle and stored at 2, 4, 9, 14, and 16 degrees C was estimated at 43, 36, 8, 5, and 3 d, respectively. For milk samples packaged in LDPE pouch, shelf life was estimated at 37, 35, 7, 3, and 2 d, respectively. The determination of Q(10) and z values demonstrated that storage temperature has a greater influence on microbiological shelf life of pasteurized milk packaged in LDPE pouch compared to HDPE bottle. Based on the results of this study, HDPE bottle was better for storing pasteurized milk as compared to LDPE pouch.

Adapting Web content for low-literacy readers by using lexical elaboration and named entities labeling

This paper presents an approach for assisting low-literacy readers in accessing Web online information. The oEducational FACILITAo tool is a Web content adaptation tool that provides innovative features and follows more intuitive interaction models regarding accessibility concerns. Especially, we propose an interaction model and a Web application that explore the natural language processing tasks of lexical elaboration and named entity labeling for improving Web accessibility. We report on the results obtained from a pilot study on usability analysis carried out with low-literacy users. The preliminary results show that oEducational FACILITAo improves the comprehension of text elements, although the assistance mechanisms might also confuse users when word sense ambiguity is introduced, by gathering, for a complex word, a list of synonyms with multiple meanings. This fact evokes a future solution in which the correct sense for a complex word in a sentence is identified, solving this pervasive characteristic of natural languages. The pilot study also identified that experienced computer users find the tool to be more useful than novice computer users do.

THE POINCARE-BENDIXSON THEOREM ON THE KLEIN BOTTLE FOR CONTINUOUS VECTOR FIELDS

We present a version of the Poincare-Bendixson Theorem on the Klein bottle K(2) for continuous vector fields. As a consequence, we obtain the fact that K(2) does not admit continuous vector fields having a omega-recurrent injective trajectory.

Arterial spin labeling of cerebral perfusion territories using a seperate labeling coil

Purpose: To obtain cerebral perfusion territories of the left, the right. and the posterior circulation in humans with high signal-to-noise ratio (SNR) and robust delineation. Materials and Methods: Continuous arterial spin labeling (CASL) was implemented using a dedicated radio frequency (RF) coil. positioned over the neck, to label the major cerebral feeding arteries in humans. Selective labeling was achieved by flow-driven adiabatic fast passage and by tilting the longitudinal labeling gradient about the Y-axis by theta = +/- 60 degrees. Results: Mean cerebral blood flow (CBF) values in gray matter (GM) and white matter (WM) were 74 +/- 13 mL center dot 100 g(-1) center dot minute(-1) and 14 +/- 13 mL center dot 100 g(-1) center dot minute(-1), respectively (N = 14). There were no signal differences between left and right hemispheres when theta = 0 degrees (P > 0.19), indicating efficient labeling of both hemispheres. When theta = +60 degrees, the signal in GM on the left hemisphere, 0.07 +/- 0.06%, was 92% lower than on the right hemisphere. 0.85 +/- 0.30% (P < 1 x 10(-9)). while for theta = -60 degrees, the signal in the right hemisphere. 0.16 +/- 0.13%, was 82% lower than on the contralateral side. 0.89 +/- 0.22% (P < 1 x 10(-10)). Similar attenuations were obtained in WM. Conclusion: Clear delineation of the left and right cerebral perfusion territories was obtained, allowing discrimination of the anterior and posterior circulation in each hemisphere.

Fixed points on Klein bottle fiber bundles over the circle

The main purpose of this work is to study fixed points of fiber-preserving maps over the circle S(1) for spaces which are fiber bundles over S(1) and the fiber is the Klein bottle K. We classify all such maps which can be deformed fiberwise to a fixed point free map. The similar problem for torus fiber bundles over S(1) has been solved recently.

Coincidence properties for maps from the torus to the Klein bottle

The authors study the coincidence theory for pairs of maps from the Torus to the Klein bottle. Reidemeister classes and the Nielsen number are computed, and it is shown that any given pair of maps satisfies the Wecken property. The 1-parameter Wecken property is studied and a partial negative answer is derived. That is for all pairs of coincidence free maps a countable family of pairs of maps in the homotopy class is constructed such that no two members may be joined by a coincidence free homotopy.