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Quantitative Features (quantitative + feature)
Selected AbstractsConstruction of quantitative proteome reference maps of mouse spleen and lymph node based on two-dimensional gel electrophoresisPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 13 2006Yayoi Kimura Abstract Quantitative features of the proteome are extremely useful for studying cellular processes at a molecular level. In this study, we attempted to construct quantitative reference proteome maps of the mouse spleen and lymph node based on 2-DE followed by protein identification using MS. We analyzed more than 1000,spots on the 2-DE images and consequently were able to determine that 919,spots were derived from 328,different genes. To obtain statistically reliable information of the protein levels from these 2-DE images, we measured the volumes of the respective spots on 2-DE images obtained by four to six independent experimental runs. These measurements were used to calculate the variability of the volumes of the respective spots on 2-DE following subcellular fractionation, which enabled us to discriminate differentially produced proteins from those within the range of intrinsic variability. More importantly, while the 2-DE data have been traditionally collected in a gel image-based manner, the resultant quantitative 2-DE data could be analyzed using the same procedure as that for mRNA expression profiles. This greatly assists in bridging the gap between the analyses of transcriptomes and proteomes and enables the integration of this data on the same informational platform. [source] Hormesis: Why it is important to toxicology and toxicologists,ENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 7 2008Edward J. Calabrese Abstract This article provides a comprehensive review of hormesis, a dose-response concept that is characterized by a low-dose stimulation and a high-dose inhibition. The article traces the historical foundations of hormesis, its quantitative features and mechanistic foundations, and its risk assessment implications. The article indicates that the hormetic dose response is the most fundamental dose response, significantly outcompeting other leading dose-response models in large-scale, head-to-head evaluations. The hormetic dose response is highly generalizable, being independent of biological model, endpoint measured, chemical class, and interindividual variability. Hormesis also provides a framework for the study and assessment of chemical mixtures, incorporating the concept of additivity and synergism. Because the hormetic biphasic dose response represents a general pattern of biological responsiveness, it is expected that it will become progressively more significant within toxicological evaluation and risk assessment practices as well as have numerous biomedical applications. [source] A comparison of three noise reduction procedures applied to bird vocal signalsJOURNAL OF FIELD ORNITHOLOGY, Issue 3 2007Myron C. Baker ABSTRACT Recordings of avian vocal signals in natural habitats include ambient noise. Often this background noise corrupts across all frequencies and is of substantial amplitude. Reducing this ambient noise to prepare vocal signals for playback stimuli or to remove habitat-specific noise signatures prior to analyzing a signal's acoustic characteristics can be useful. We conducted experimental evaluations of three noise reduction procedures to determine their effectiveness. We embedded two bird vocalizations ("clean" signals) in four kinds of natural noise, resulting in eight noise-signal combinations. We then applied three noise reduction procedures (Noise Profile, Band Pass, and Noise Estimate) to each of the embedded signals and compared the recovered signals to the original (clean) signals. Noise Profile filtering was effective in reducing noise and returning fairly high-quality signals from even severe levels of masking noise. The other two noise reduction procedures did not perform as well. For the two most corrupting maskers, however, Noise Profile filtering also altered the signal properties by reducing signal amplitude at those frequencies containing high levels of noise. Apart from this loss of amplitude, the quantitative features of the filtered signals were similar to those of the original model sounds. We conclude that Noise Profile filtering produces good results for cases where noise is approximately constant over the signal duration and the signal intensity exceeds noise intensity over the frequencies of interest. SINOPSIS La grabación de sonidos de aves en hábitats naturales incluye ruidos ambientales. A menudo este ruido es de amplitud sustancial y afecta todas las frecuencias. Antes de analizar una señal vocal, podría ser útil reducir este ruido ambiental, bien para preparar vocalizaciones grabadas para provocar respuestas de aves como para remover ruidos asociados a hábitats. Llevamos a cabo una serie de experimentos con tres procedimientos de reducción de ruido para determinar su efectividad. Insertamos dos vocalizaciones de aves (señales "limpias") en cuatro tipos de ruidos naturales, obteniendo como resultado ocho combinaciones de señales con ruido. Posteriormente, aplicamos tres procedimientos de reducción de ruido ("Perfil de Ruido,""Paso de Banda" y "Estimaciones de Ruido") a cada una de las señales insertadas y comparamos las señales recuperadas con los sonidos originales (limpios). La filtración tipo "Perfil de Ruido" resultó efectiva para reducir el ruido y producir señales de razonablemente buena calidad, aún en situaciones de ruido severo. Los otros dos tratamientos no funcionaron tan bien. Para los dos tipos de ruido con mayores efectos, el "Perfil de Ruido" alteró las propiedades de la señal y redujo la amplitud de la misma, en aquellas frecuencias que contenían altos niveles de ruido. Además de la pérdida de amplitud, los elementos cuantitativos de las señales filtradas fueron similares a las de los modelos sonoros originales. Concluimos que el procedimiento de filtrado "Perfil de Ruido" produce buenos resultados para casos en donde el ruido es de duración aproximadamente constante a lo largo de la señal y cuando la intensidad de la señal excede la intensidad del ruido sobre las frecuencias de interés. [source] Automatic analysis of aqueous specimens for phytoplankton structure recognition and population estimationMICROSCOPY RESEARCH AND TECHNIQUE, Issue 9 2006Karsten Rodenacker Abstract An automatic microscope image acquisition, evaluation, and recognition system was developed for the analysis of Utermöhl plankton chambers in terms of taxonomic algae recognition. The system called PLASA (Plankton Structure Analysis) comprises (1) fully automatic archiving (optical fixation) of aqueous specimens as digital bright field and fluorescence images, (2) phytoplankton analysis and recognition, and (3) training facilities for new taxa. It enables characterization of aqueous specimens by their populations. The system is described in detail with emphasis on image analytical aspects. Plankton chambers are scanned by sizable grids, divers objective(s), and up to four fluorescence spectral bands. Acquisition positions are focused and digitized by a TV camera and archived on disk. The image data sets are evaluated by a large set of quantitative features. Automatic classifications for a number of organisms are developed and embedded in the program. Interactive programs for the design of training sets were additionally implemented. A long-term sampling period of 23 weeks from two ponds at two different locations each was performed to generate a reliable data set for training and testing purposes. These data were used to present this system's results for phytoplankton structure characterization. PLASA represents an automatic system, comprising all steps from specimen processing to algae identification up to species level and quantification. Microsc. Res. Tech., 2006. © 2006 Wiley-Liss, Inc. [source] Signal Processing during Developmental Multicellular PatterningBIOTECHNOLOGY PROGRESS, Issue 1 2008Claudiu A. Giurumescu Developing design strategies for tissue engineering and regenerative medicine is limited by our nascent understanding of how cell populations "self-organize" into multicellular structures on synthetic scaffolds. Mechanistic insights can be gleaned from the quantitative analysis of biomolecular signals that drive multicellular patterning during the natural processes of embryonic and adult development. This review describes three critical layers of signal processing that govern multicellular patterning: spatiotemporal presentation of extracellular cues, intracellular signaling networks that mediate crosstalk among extracellular cues, and finally, intranuclear signal integration at the level of transcriptional regulation. At every level in this hierarchy, the quantitative attributes of signals have a profound impact on patterning. We discuss how experiments and mathematical models are being used to uncover these quantitative features and their impact on multicellular phenotype. [source] Phylogeny of the genus Palmanura (Collembola: Neanuridae)CLADISTICS, Issue 5 2010José G. Palacios Vargas In order to assess the phylogenetic structure of the springtail genus Palmanura, as well as to test the monophyly of the tribe Sensillanurini (Neanuridae: Neanurinae), a data matrix of morphological (chaetotactic and other) characters of members of this group was assembled and analysed in the light of Wagner parsimony. The data matrix included all the known members of the Neotropical genus Palmanura, plus representatives of Sensillanura and Americanura. Although not all the clades obtained were highly supported by bootstrap resampling, some structures were relatively constant under different approaches. Alternative analyses (unordered and ordered character states, rescaled weighting procedure) were applied. While alternative solutions were obtained, a number of structures were shared by the results irrespective of the method used. On this basis, the results suggest that some further reassessment is required to confirm formally the monophyly of the tribe Sensillanurini. The genera Palmanura and Americanura are mutually poly/paraphyletic; we thus suggest that Palmanura should be considered as a synonym of Americanura, although some character reassessment and more varied outgroup species may be necessary before a formal generic redefinition can be proposed. Finally, a comparison of the performance of the characters under Wagner parsimony analysis indicated that differences in the characters' retention indexes are due not to the topological (tagmal) position of the traits involved, but to character coding: the characters describing quantitative features (generally numbers of setae) generally performed worse than other types of characters under parsimony. An updated list of the known members of the Sensillanurini (Collembola: Neanuridae: Neanurinae) is presented. © The Willi Hennig Society 2009. [source] | ||||||||||