DNA ANALYSIS USING GRAMMATICAL INFERENCE

An accurate language definition capable of distinguishing between coding and non-coding DNA has important applications and analytical significance to the field of computational biology. The method proposed here uses positive sample grammatical inference and statistical information to infer languages for coding DNA. An algorithm is proposed for the searching of an optimal subset of input sequences for the inference of regular grammars by optimizing a relevant accuracy metric. The algorithm does not guarantee the finding of the optimal subset; however, testing shows improvement in accuracy and performance over the basis algorithm. Testing shows that the accuracy of inferred languages for components of DNA are consistently accurate. By using the proposed algorithm languages are inferred for coding DNA with average conditional probability over 80%. This reveals that languages for components of DNA can be inferred and are useful independent of the process that created them. These languages can then be analyzed or used for other tasks in computational biology. To illustrate potential applications of regular grammars for DNA components, an inferred language for exon sequences is applied as post processing to Hidden Markov exon prediction to reduce the number of wrong exons detected and improve the specificity of the model significantly

Effects of various anthropometric measurements on fastball velocity in professional relief pitchers.

This research study was conducted to compare the height and weights of Major League Baseball (MLB) relief pitchers to their average fastball velocity during the 2007 season. The purpose was to find what correlations may exist between each independent variableand the dependent variable. In essence, how well does height and weight predict average fastball velocity? The participants included qualifying MLB relief pitchers that finished in the top seventy-five of average fastball velocity. Data was collected from Baseball Info Solutions regarding height, weight, and fastball velocity and placed into IBM's SPSS statistical analysis software. The statistical technique used to analyze the data was multiple regression with a set wise progression. The overall model displayed no significant correlation (r value; 0.131, p value; .535) and also showed that the independent variables accounted for only 1.7% of the dependent variable's value (R2 = .017). The mean average fastball velocity was 93.256 mph while average heights and weights of the players were, 189.68cm, and 97.35kg, respectively. Results showed that there was no significant correlation between fastball velocity and weight (r value;0.132) or height (r value; 0.380). While there were no significant correlations found in the general anthropometric measurements used there may be other predictors present that can better account for average fastball velocity. Future research is needed to find these predictors and what affect they have on the ability to throw with a high velocity

Applying a qualitative framework of acceptance of personal robots

Personal robots can help people live safer, more efficient and comfortable lives. However, such benefits cannot be achieved if people do not use, or accept, personal robots. The use of a technology is predominantly influenced by an individual's intention to use it, which is influenced by his or her attitudes toward it (Davis, 1989). Presently, the key factors that impact the use of personal robots are not fully understood. Two studies were conducted as first step assessments of the Smarr, Fisk, and Rogers (2013) theoretically-based framework of acceptance of personal robots. In study 1, 14 participants used a personal robot (a robot lawn mower) at their homes for about six weeks. Their acceptance and factors important for acceptance identified in the framework were measured using pre-use and post-use interviews and questionnaires, and weekly diaries. The framework was conceptually validated; participants mentioned 16 of the 20 factors in the Smarr et al. (2013) framework. However, the framework did not fully account for the breadth of factors discussed by participants, thereby suggesting variables may need to be added to or removed from the framework. In study 2, 280 participants reported their initial acceptance of a personal robot (a robot mower) with different levels of reliability and communication of feedback in an online survey. Level of robot reliability did significantly affect attitudinal and intentional acceptance. Follow up analyses indicated a trend that participants who received no information on reliability had numerically higher acceptance than participants who were informed that the robot had 70% reliability or 90% reliability. Neither communication of feedback nor its interaction with reliability affected acceptance. The Smarr et al. (2013) framework explained about 60% of the variance in intentional acceptance and 57% in attitudinal acceptance of a personal robot. Eight of the 15 relationships tested were supported via path analysis. Findings largely supported the Smarr et al. (2013) framework in explaining what impacts intentional and attitudinal acceptance of a personal robot. Results from these studies can inform the Smarr et al. (2013) framework of robot acceptance and other models of acceptance, and can guide designers in developing acceptable personal robots.Ph.D

The chemokine receptor CCR6 is an important component of the innate immune response

In our initial studies we found that naÏve CCR6-deficient (CCR6 –/– ) C57BL/6 mice possessed significantly lower number of both F4/80 + macrophages and dendritic cells (DC), but higher number of B cells in the peritoneal cavity, as compared to naÏve wild type (WT) controls. Furthermore, peritoneal macrophages isolated from CCR6 –/– mice expressed significantly lower levels of inflammatory cytokines and nitric oxide following lipopolysaccharide (LPS)stimulation, as compared to WT macrophages. In a severe experimental peritonitis model induced by cecal ligation and puncture (CLP), CCR6 –/– mice were protected when compared with WT controls. At 24 h following the induction of peritonitis, CCR6 –/– mice exhibited significantly lower levels of inflammatory cytokines/chemokines in both the peritoneal cavity and blood. Interestingly, DC recruitment into the peritoneal cavity was impaired in CCR6 –/– mice during the evolution of CLP-induced peritonitis. Peritoneal macrophages isolated from surviving CCR6 –/– mice 3 days after CLP-induced peritonitis exhibited an enhanced LPS response compared with similarly treated WT peritoneal macrophages. These data illustrate that CCR6 deficiency alters the innate response via attenuating the hyperactive local and systemic inflammatory response during CLP-induced peritonitis.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/56112/1/2487_ftp.pd

Nanoparticles modified with multiple organic acids

Surface-modified nanoparticles of boehmite, and methods for preparing the same. Aluminum oxyhydroxide nanoparticles are surface modified by reaction with selected amounts of organic acids. In particular, the nanoparticle surface is modified by reactions with two or more different carboxylic acids, at least one of which is an organic carboxylic acid. The product is a surface modified boehmite nanoparticle that has an inorganic aluminum oxyhydroxide core, or part aluminum oxyhydroxide core and a surface-bonded organic shell. Organic carboxylic acids of this invention contain at least one carboxylic acid group and one carbon-hydrogen bond. One embodiment of this invention provides boehmite nanoparticles that have been surface modified with two or more acids one of which additional carries at least one reactive functional group. Another embodiment of this invention provides boehmite nanoparticles that have been surface modified with multiple acids one of which has molecular weight or average molecular weight greater than or equal to 500 Daltons. Yet, another embodiment of this invention provides boehmite nanoparticles that are surface modified with two or more acids one of which is hydrophobic in nature and has solubility in water of less than 15 by weight. The products of the methods of this invention have specific useful properties when used in mixture with liquids, as filler in solids, or as stand-alone entities

Time Dynamics of Self-Pumped Reflection Gratings in a Photorefractive Polymer

The time dynamics of self-pumped reflection gratings in a commonly used photorefractive polymer PDCST:PVK:ECZ-BBP:C60 with no additional electron sources or traps is investigated. While holes are normally the mobile charges and responsible for grating formation, our experimental observations, analyzed using multi-exponential fitting curves, show evidence of electrons in addition to holes as charge carriers, particularly above an applied field of 40 V/μm. The dependence of effective carrier mobilities on the applied electric field, deduced from experimental results, show stronger field dependence of electron mobility at high electric fields. At an applied field of 70 V/μm, electron and hole mobilities become approximately equal, and the contribution of electrons on grating formation becomes significant

Control of Decoherence: Dynamical Decoupling versus Quantum Zeno Effect - a case study for trapped ions

The control of thermal decoherence via dynamical decoupling and via the quantum Zeno effect (Zeno control) is investigated for a model of trapped ion, where the dynamics of two low lying hyperfine states undergoes decoherence due to the thermal interaction with an excited state. Dynamical decoupling is a procedure that consists in periodically driving the excited state, while the Zeno control consists in frequently measuring it. When the control frequency is high enough, decoherence is shown to be suppressed. Otherwise, both controls may accelerate decoherence.Comment: 24 pages, 8 figure

BCMA Is Essential for the Survival of Long-lived Bone Marrow Plasma Cells

Long-lived humoral immunity is manifested by the ability of bone marrow plasma cells (PCs) to survive for extended periods of time. Recent studies have underscored the importance of BLyS and APRIL as factors that can support the survival of B lineage lymphocytes. We show that BLyS can sustain PC survival in vitro, and this survival can be further enhanced by interleukin 6. Selective up-regulation of Mcl-1 in PCs by BLyS suggests that this α-apoptotic gene product may play an important role in PC survival. Blockade of BLyS, via transmembrane activator and cyclophilin ligand interactor–immunoglobulin treatment, inhibited PC survival in vitro and in vivo. Heightened expression of B cell maturation antigen (BCMA), and lowered expression of transmembrane activator and cyclophilin ligand interactor and BAFF receptor in PCs relative to resting B cells suggests a vital role of BCMA in PC survival. Affirmation of the importance of BCMA in PC survival was provided by studies in BCMA−/− mice in which the survival of long-lived bone marrow PCs was impaired compared with wild-type controls. These findings offer new insights into the molecular basis for the long-term survival of PCs

Barley grain (1,3;1,4)-β-glucan content:effects of transcript and sequence variation in genes encoding the corresponding synthase and endohydrolase enzymes

The composition of plant cell walls is important in determining cereal end uses. Unlike other widely consumed cereal grains barley is comparatively rich in (1,3;1,4)-β-glucan, a source of dietary fibre. Previous work showed Cellulose synthase-like genes synthesise (1,3;1,4)-β-glucan in several tissues. HvCslF6 encodes a grain (1,3;1,4)-β-glucan synthase, whereas the function of HvCslF9 is unknown. Here, the relationship between mRNA levels of HvCslF6, HvCslF9, HvGlbI (1,3;1,4)-β-glucan endohydrolase, and (1,3;1,4)-β-glucan content was studied in developing grains of four barley cultivars. HvCslF6 was differentially expressed during mid (8-15 DPA) and late (38 DPA) grain development stages while HvCslF9 transcript was only clearly detected at 8-10 DPA. A peak of HvGlbI expression was detected at 15 DPA. Differences in transcript abundance across the three genes could partially explain variation in grain (1,3;1,4)-β-glucan content in these genotypes. Remarkably narrow sequence variation was found within the HvCslF6 promoter and coding sequence and does not explain variation in (1,3;1,4)-β-glucan content. Our data emphasise the genotype-dependent accumulation of (1,3;1,4)-β-glucan during barley grain development and a role for the balance between hydrolysis and synthesis in determining (1,3;1,4)-β-glucan content, and suggests that other regulatory sequences or proteins are likely to be involved in this trait in developing grain.Guillermo Garcia-Gimenez, Joanne Russell, Matthew K. Aubert, Geoffrey B. Fincher, Rachel A. Burton, Robbie Waugh, Matthew R. Tucker, Kelly Housto