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Search Results: 1 - 10 of 406694 matches for " Denise M. Wolf "
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Memory in Microbes: Quantifying History-Dependent Behavior in a Bacterium
Denise M. Wolf, Lisa Fontaine-Bodin, Ilka Bischofs, Gavin Price, Jay Keasling, Adam P. Arkin
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0001700
Abstract: Memory is usually associated with higher organisms rather than bacteria. However, evidence is mounting that many regulatory networks within bacteria are capable of complex dynamics and multi-stable behaviors that have been linked to memory in other systems. Moreover, it is recognized that bacteria that have experienced different environmental histories may respond differently to current conditions. These “memory” effects may be more than incidental to the regulatory mechanisms controlling acclimation or to the status of the metabolic stores. Rather, they may be regulated by the cell and confer fitness to the organism in the evolutionary game it participates in. Here, we propose that history-dependent behavior is a potentially important manifestation of memory, worth classifying and quantifying. To this end, we develop an information-theory based conceptual framework for measuring both the persistence of memory in microbes and the amount of information about the past encoded in history-dependent dynamics. This method produces a phenomenological measure of cellular memory without regard to the specific cellular mechanisms encoding it. We then apply this framework to a strain of Bacillus subtilis engineered to report on commitment to sporulation and degradative enzyme (AprE) synthesis and estimate the capacity of these systems and growth dynamics to ‘remember’ 10 distinct cell histories prior to application of a common stressor. The analysis suggests that B. subtilis remembers, both in short and long term, aspects of its cell history, and that this memory is distributed differently among the observables. While this study does not examine the mechanistic bases for memory, it presents a framework for quantifying memory in cellular behaviors and is thus a starting point for studying new questions about cellular regulation and evolutionary strategy.
Gene Co-Expression Modules as Clinically Relevant Hallmarks of Breast Cancer Diversity
Denise M. Wolf, Marc E. Lenburg, Christina Yau, Aaron Boudreau, Laura J. van ‘t Veer
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0088309
Abstract: Co-expression modules are groups of genes with highly correlated expression patterns. In cancer, differences in module activity potentially represent the heterogeneity of phenotypes important in carcinogenesis, progression, or treatment response. To find gene expression modules active in breast cancer subpopulations, we assembled 72 breast cancer-related gene expression datasets containing ~5,700 samples altogether. Per dataset, we identified genes with bimodal expression and used mixture-model clustering to ultimately define 11 modules of genes that are consistently co-regulated across multiple datasets. Functionally, these modules reflected estrogen signaling, development/differentiation, immune signaling, histone modification, ERBB2 signaling, the extracellular matrix (ECM) and stroma, and cell proliferation. The Tcell/Bcell immune modules appeared tumor-extrinsic, with coherent expression in tumors but not cell lines; whereas most other modules, interferon and ECM included, appeared intrinsic. Only four of the eleven modules were represented in the PAM50 intrinsic subtype classifier and other well-established prognostic signatures; although the immune modules were highly correlated to previously published immune signatures. As expected, the proliferation module was highly associated with decreased recurrence-free survival (RFS). Interestingly, the immune modules appeared associated with RFS even after adjustment for receptor subtype and proliferation; and in a multivariate analysis, the combination of Tcell/Bcell immune module down-regulation and proliferation module upregulation strongly associated with decreased RFS. Immune modules are unusual in that their upregulation is associated with a good prognosis without chemotherapy and a good response to chemotherapy, suggesting the paradox of high immune patients who respond to chemotherapy but would do well without it. Other findings concern the ECM/stromal modules, which despite common themes were associated with different sites of metastasis, possibly relating to the “seed and soil” hypothesis of cancer dissemination. Overall, co-expression modules provide a high-level functional view of breast cancer that complements the “cancer hallmarks” and may form the basis for improved predictors and treatments.
Differences in Mean Number of Consonant-Vowel-Consonant Words Decoded between Letter-Sound Readers and Non Letter-Sound Readers  [PDF]
Gail M. Wolf
Open Journal of Nursing (OJN) , 2014, DOI: 10.4236/ojn.2014.46047
Abstract:

Children’s failure to develop simple word decoding skills in early years is linked to future poor reading, school dropout, and poor health [1] [2]. Letter-sound knowledge is needed for word decoding development; however questions remain on what types of letter-sound knowledge help children decode simple words [3]. This study investigated the differences in mean number of consonant-vowel-consonant (CVC) words decoded between two groups of children, a letter-sound reading group and non letter-sound reading group. Children aged 4 to 6 in both groups, attempted to decode a variety of simple words such as tan, sit, hen, pig, dot, and fun. Analysis determined word decoding differences existed between the two groups. The alternate hypothesis was accepted; the letter-sound reading group had a significantly higher mean in number of consonant-vowel-consonant words decoded compared to the non letter-sound reading group. The study informs the teaching approaches needed to

Developing Reading Automaticity and Fluency: Revisiting What Reading Teachers Know, Putting Confirmed Research into Current Practice  [PDF]
Gail M. Wolf
Creative Education (CE) , 2018, DOI: 10.4236/ce.2018.96062
Abstract: This article revisits research on reading automaticity and fluency with the goal of helping beginning reading teachers put confirmed research findings into current classroom practice. The article examines the concepts of automaticity and fluency, how both impact the development of skillful reading. The article reviews research on: a) reading strategies children use, and b) repeat reading teaching strategies to develop fluency. Case scenarios illustrate key findings. Based on the research and case scenarios, four conclusions are drawn: 1) The terms automaticity and fluency are often interchanged; the concepts are not the same; 2) Understanding the differences between automaticity and fluency can impact repeat reading teaching strategies; 3) There is an assumption that rapid word recognition is the same cognitive process as automatic word decoding; and 4) There are two pathways to fluent reading, rapid word recognition, and automatic decoding ability. The article presents a theoretical model which aligns with childhood learning theories, offering teachers a variation in repeat reading teaching strategies. Rather than repeating reading the same text, opportunities to read slightly different, decodable text improves decoding, builds fluency, and thus strengthens children’s reading comprehension of complex text.
The Influence of Air-Abrasive Trimming on the Current Noise of Thick Film Resistors
M. Wolf
Active and Passive Electronic Components , 1984, DOI: 10.1155/apec.11.157
Abstract:
Earth Inner Core Periodic Motion due to Pressure Difference Induced by Tidal Acceleration
M. Wolf
Physics , 2013,
Abstract: The inner structure of the earth is still a topic of discussion. Seismic measurements showed a structure of solid, liquid, solid which describes the mantle, outer core and inner core with the inner core in the center. The analysis of waveform doublets suggests now that the inner core is out of center and even of faster rotation than the mantel and crust. From the sum of Buoyancy and Gravity on the earth inner core, the position energy is plotted and together with the tangential tidal acceleration, it is derived that Earth Inner Core cannot be in a center position without additional force. The Earth Core System is explained as Hydrodynamic Bearing. The tidal acceleration is identified as the reason for the periodic motion of the inner core and certain frequencies of nutation. The Eccentricities out of nutation due to the effects from the sun and moon are calculated as an approximation.
On Experimental Data of the TCR of TFRs and Their Relation to Theoretical Models of Conduction Mechanism
I. Storbeck,M. Wolf
Active and Passive Electronic Components , 1985, DOI: 10.1155/apec.11.255
Abstract:
About the Influence of SiO2 on the Temperature Behaviour of Ruthenate Based Thick Film Resistors
I. Storbeck,M. Wolf
Active and Passive Electronic Components , 1987, DOI: 10.1155/1987/41585
Abstract:
Not-so-normal mode decomposition
Michael M. Wolf
Physics , 2007, DOI: 10.1103/PhysRevLett.100.070505
Abstract: We provide a generalization of the normal mode decomposition for non-symmetric or locality constrained situations. This allows for instance to locally decouple a bipartitioned collection of arbitrarily correlated oscillators up to elementary pairs into which all correlations are condensed. Similarly, it enables us to decouple the interaction parts of multi-mode channels into single-mode and pair-interactions where the latter are shown to be a clear signature of squeezing between system and environment. In mathematical terms the result is a canonical matrix form with respect to real symplectic equivalence transformations.
Apsidal motion and absolute parameters for five LMC eccentric eclipsing binaries
P. Zasche,M. Wolf
Physics , 2013, DOI: 10.1051/0004-6361/201322054
Abstract: Aims: As part of our observational projects at the La Silla Danish 1.54-meter telescope, we aim to measure the precise times of minimum light for eccentric eclipsing binaries in the Large Magellanic Cloud, needed for accurate determination of apsidal motion. Many new times of minima were derived from the photometric databases OGLE and MACHO. Several new minima were also observed. Five early-type and eccentric-orbit eclipsing binaries: HV 982 (P = 5.34 d, e = 0.15), HV 2274 (5.73 d, 0.17), MACHO 78.6097.13 (3.11 d, 0.05), MACHO 81.8881.47 (3.88 d, 0.22), and MACHO 79.5377.76 (2.64 d, 0.06) were studied. Methods: The O-C diagrams of the systems were analysed using all reliable timings found in the literature, and new or improved elements of apsidal motion were obtained. Light and radial velocity curves of MACHO 81.8881.47 and MACHO 79.5377.76 were analysed using the program PHOEBE. Results: We derived for the first time or significantly improved the relatively short periods of apsidal motion of 211 (12), 127 (8), 48 (13), 103 (20), and 42 (19) years, respectively. The internal structure constants, log k2, were found to be -2.37, -2.47, -2.17, -2.02, and -1.86 respectively, under the assumption that the component stars rotate pseudosynchronously. The relativistic effects are weak, up to 6% of the total apsidal motion rate. The masses for MACHO 81.8881.47 resulted in 5.51 (0.21) and 5.40 (0.19) M0, while for MACHO 79.5377.76 the masses are 11.26 (0.35) and 11.27 (0.35) M0, respectively.
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