A Model Of Visual Recognition Implemented Using Neural Networks

The ability to recognise and classify objects in the environment is an important property of biological vision. It is highly desirable that artificial vision systems also have this ability. This thesis documents research into the use of artificial neural networks to implement a prototype model of visual object recognition. The prototype model, describing a computtional architecture, is derived from relevant physiological and psychological data, and attempts to resolve the use of structural decomposition and invariant feature detection. To validate the research a partial implementation of the model has been constructed using multiple neural networks. A linear feed-forward network performs pre-procesing after being trained to approximate a conventional statistical data compression algorithm. The output of this pre-processing forms a feature vector that is categorised using an Adaptive Resonance Theory network capable of recognising arbitrary analog patterns. The implementation has been applied to the task of recognising static images of human faces. Experimental results show that the implementation is able to achieve a 100% successful recognition rate with performance that degrades gracefully. The implentation is robust against facial changes minor occlusions and it is flexible enough to categorise data from any domain

An improved method for surface immobilisation of RNA: application to small Non-Coding RNA - mRNA pairing

Characterisation of RNA and its intermolecular interactions is increasing in importance as the inventory of known RNA functions continues to expand. RNA-RNA interactions are central to post-transcriptional gene regulation mechanisms in bacteria, and the interactions of bacterial small non-coding RNAs (sRNAs) with their mRNA targets are the subject of much current research. The technology of surface plasmon resonance (SPR) is an attractive approach to studying these interactions since it is highly sensitive, and allows interaction measurements to be recorded in real-time. Whilst a number of approaches exist to label RNAs for surface-immobilisation, the method documented here is simple, quick, efficient, and utilises the high-affinity streptavidin-biotin interaction. Specifically, we ligate a biotinylated nucleotide to the 3' end of RNA using T4 RNA ligase. Although this is a previously recognised approach, we have optimised the method by our discovery that the incorporation of four or more adenine nucleotides at the 3' end of the RNA (a poly-A-tail) is required in order to achieve high ligation efficiencies. We use this method within the context of investigating small non-coding RNA (sRNA)-mRNA interactions through the application of surface technologies, including quantitative SPR assays. We first focus on validating the method using the recently characterised Escherichia coli sRNA-mRNA pair, MicA-ompA, specifically demonstrating that the addition of the poly-A-tail to either RNA does not affect its subsequent binding interactions with partner molecules. We then apply this method to investigate the novel interactions of a Vibrio cholerae Qrr sRNA with partner mRNAs, hapR and vca0939; RNA-RNA pairings that are important in mediating pathogenic virulence. The calculated binding parameters allow insights to be drawn regarding sRNA-mRNA interaction mechanisms

Stochastic Simulation of Process Calculi for Biology

Biological systems typically involve large numbers of components with complex, highly parallel interactions and intrinsic stochasticity. To model this complexity, numerous programming languages based on process calculi have been developed, many of which are expressive enough to generate unbounded numbers of molecular species and reactions. As a result of this expressiveness, such calculi cannot rely on standard reaction-based simulation methods, which require fixed numbers of species and reactions. Rather than implementing custom stochastic simulation algorithms for each process calculus, we propose to use a generic abstract machine that can be instantiated to a range of process calculi and a range of reaction-based simulation algorithms. The abstract machine functions as a just-in-time compiler, which dynamically updates the set of possible reactions and chooses the next reaction in an iterative cycle. In this short paper we give a brief summary of the generic abstract machine, and show how it can be instantiated with the stochastic simulation algorithm known as Gillespie's Direct Method. We also discuss the wider implications of such an abstract machine, and outline how it can be used to simulate multiple calculi simultaneously within a common framework.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005

Prevalence of Noise-Induced Hearing Loss in Student Musicians

Abstract: This study describes the prevalence and characteristics of noise-induced hearing loss (NIHL) in student musicians (N = 329) aged 18-25 years. Students completed a questionnaire regarding exposures before a hearing assessment. NIHL was defined by the presence of a notch 15 dB in depth at 4000 or 6000 Hz relative to the best preceding threshold. Overall prevalence of NIHL was 45%, with 78% of notches occurring at 6000 Hz. The proportion of the total population with bilateral notching at any frequency was 11.5%, mostly occurring at 6000 Hz. There was a significant increase in the frequency of notching in students who reported more than two hours per day of personal practice. There were no significant associations for instrument group or other noise exposures. The data suggest that susceptibility to NIHL among students of music is not uniform and cannot be ascribed solely to the instrument played and other exposures. Students with bilateral losses tend to have deeper notches and may represent a group that has an inherent predisposition to NIHL. Sumario Este estudio describe la prevalencia y las características de la hipoacusia inducida por ruido (NIHL) en estudiantes de música (N = 329) con edades entre 18 y 25 años. Los estudiantes completaron un cuestionario sobre exposición a ruido antes de la evaluación auditiva. Se definió NIHL como la presencia de una muesca de 15dB en 4000 o 6000Hz con relación al mejor umbral precedente. La prevalencia general de NIHL fue de 44%, con 78% de las muescas en 6,000 Hz. La proporción de la población total con muescas bilaterales en cualquier frecuencia fue de 11.5%, en su mayoría a 6,000 Hz. Hubo un incremento significativo en la frecuencia de la muescas en los estudiantes que reportaban más de dos horas al día de práctica profesional. No hubo una asociación significativa con grupos de instrumentos u otra exposición a ruido. Los datos sugieren que la susceptibilidad a NIHL entre los estudiantes de música no es uniforme y no puede atribuirse solamente al instrumento tocado o a otras exposiciones. Los estudiantes con pérdida bilateral tienden a tener muescas más profundas y pueden representar un grupo que tenga una predisposición inherente a la NIHL. Keywords: Noise-induced hearing loss, Music-related hearing loss, Prevalence of hearing loss, Predisposition Article: Noise-induced hearing loss (NIHL) is the most prevalent sensorineural hearing loss after presbycusis. Prevalence of NIHL increases with continued exposure and advancing age. The prevention of NIHL will require a better understanding of its prevalence in the population and contributing exposure factors. NIHL can be caused by a single traumatic impulse sound but is more typically caused by repeated exposures to high intensity sound. According to NIOSH recommendations for the prevention of NIHL, high intensity sound exposure involves a time-intensity trade-off that begins with an allowable eight-hour exposure at 85 dBA, decreasing the time exposed by half for every three dB increase in intensity. Sound exposure measurements in music students and music teachers document exposure levels over 85 dB

Nuclear hyaluronidase 2 drives alternative splicing of CD44 pre-mRNA to determine profibrotic or antifibrotic cell phenotype

The cell surface protein CD44 is involved in diverse physiological processes, and its aberrant function is linked to various pathologies such as cancer, immune dysregulation, and fibrosis. The diversity of CD44 biological activity is partly conferred by the generation of distinct CD44 isoforms through alternative splicing. We identified an unexpected function for the ubiquitous hyaluronan-degrading enzyme, hyaluronidase 2 (HYAL2), as a regulator of CD44 splicing. Standard CD44 is associated with fibrotic disease, and its production is promoted through serine-arginine–rich (SR) protein–mediated exon exclusion. HYAL2 nuclear translocation was stimulated by bone morphogenetic protein 7, which inhibits the myofibroblast phenotype. Nuclear HYAL2 displaced SR proteins from the spliceosome, thus enabling HYAL2, spliceosome components (U1 and U2 small nuclear ribonucleoproteins), and CD44 pre-mRNA to form a complex. This prevented double-exon splicing and facilitated the inclusion of CD44 exons 11 and 12, which promoted the accumulation of the antifibrotic CD44 isoform CD44v7/8 at the cell surface. These data demonstrate previously undescribed mechanisms regulating CD44 alternative splicing events that are relevant to the regulation of cellular phenotypes in progressive fibrosis

Variable Magnitude and Frequency Financial Reinforcement is Effective at Increasing Adults’ Free-Living Physical Activity

Financial rewards can increase health behaviors, but little research has quantified the effects of different reinforcement schedules on this process. This analysis compares the average moderate-to-vigorous physical activity (MVPA) associated with six distinct positive reinforcement schedules implemented within a physical activity promotion clinical trial. In this trial, participants (N = 512) wore an accelerometer for 1 year and were prescribed one of two types of MVPA goals: a static 30-min goal or an adaptive goal based on the MVPA produced over the previous 9 days. As participants met goals, they transitioned through a sequence of reinforcement stages, beginning with a continuous-fixed magnitude (CRF-FM), then CRF-variable magnitude (CRF-VM), followed by a series of variable ratio-VM (VR-VM) schedules. The average accumulation of MVPA bouts over the last 24 days of each stage was compared to each other. Average MVPA during stage transitions was also examined. The results indicated that immediate reinforcement resulted in more MVPA relative to a comparison group and that the relative effectiveness of adaptive versus static goals was dependent on the magnitude of daily MVPA goals. Schedule effects were qualitatively different for individuals who frequently met their daily goals (Large Intervention Effect subgroup) versus those who did not (Small Intervention Effect subgroup). For the Large Intervention Effect group, the CRF-VM schedule produced the most MVPA, in particular within the adaptive goal condition, with increases observed immediately upon encountering this schedule. In contrast, the CRF-FM schedule produced small amounts of MVPA. This pattern was reversed for the Small Intervention Effect subgroup, where the most MVPA was associated with the CRF-FM stage. Future interventions should focus on discriminating small versus large intervention effects as quickly as possible so that the optimal reinforcement schedule can be used

Correction to: Variable Magnitude and Frequency Financial Reinforcement is Effective at Increasing Adults’ Free-Living Physical Activity

The original article has been corrected to update figures 1, 4, and 5 captions. Original article available on Springer\u27s website or in Chapman University Digital Commons

Feasibility of a bilateral 4000–6000 Hz notch as a phenotype for genetic association analysis

Objective: Noise-induced hearing loss (NIHL) is a worldwide health problem and a growing concern among young people. Although some people appear to be more susceptible to NIHL, genetic association studies lack a specific phenotype. We tested the feasibility of a bilateral 4000–6000 Hz audiometric notch as a phenotype for identifying genetic contributions to hearing loss in young adults. Design: A case-control-control study was conducted to examine selected SNPs in 52 genes previously associated with hearing loss and/or expressed in the cochlea. A notch was defined as a minimum of a 15-dB drop at 4000–6000 Hz from the previous best threshold with a 5-dB ‘recovery’ at 8000 Hz. Study sample: Participants were 252 individuals of European descent taken from a population of 640 young adults who are students of classical music. Participants were grouped as No-notch (NN), Unilateral Notch (UN), or Bilateral Notch (BN). Results: The strongest evidence of a genetic association with the 4000–6000 Hz notch was a nonsynonymous SNP variant in the ESRR– gene (rs61742642:C> T, P386S). Carriers of the minor allele accounted for 26% of all bilateral losses. Conclusion: This study indicates that the 4000–6000 Hz bilateral notch is a feasible phenotype for identifying genetic susceptibility to hearing loss

Glacial sediments, landforms, paleosols, and a 20,000-year-old forest bed in East-Central Illinois.

"April 21, 1999."Includes bibliographical references (p. 29-31)."33rd annual meeting, April 1999 North-Central section, Geological Society of America" --cover

Hyaluronidase-2 regulates RhoA signalling, myofibroblast contractility and other key pro-fibrotic myofibroblast functions

Hyaluronidase-2 (HYAL2) is a weak, acid-active hyaluronan-degrading enzyme that is broadly expressed in somatic tissues. Aberrant HYAL2 expression is implicated in diverse pathology. However, a significant proportion of HYAL2 is enzymatically inactive, thus the mechanisms through which HYAL2 dysregulation influences pathobiology is unclear. Recently, non-enzymatic HYAL2 functions have been described and our group has shown that nuclear HYAL2 can influence mRNA splicing to prevent myofibroblast differentiation. Myofibroblasts drive fibrosis, thereby promoting progressive tissue damage and leading to multimorbidity. This study identifies a novel HYAL2 cytoplasmic function in myofibroblasts that is unrelated to its enzymatic activity. In fibroblasts and myofibroblasts HYAL2 interacts with the small GTPase signaling molecule, RhoA. Transforming Growth Factor (TGF)-β1-driven fibroblast-to-myofibroblast differentiation promotes HYAL2 cytoplasmic re-localization to bind to the actin cytoskeleton. Cytoskeletal-bound HYAL2 functions as a key regulator of downstream RhoA signaling and influences pro-fibrotic myofibroblast functions including myosin light-chain kinase (MLCK) mediated myofibroblast contractility, myofibroblast migration, myofibroblast collagen/fibronectin deposition, as well as connective tissue growth factor (CTGF/CCN2) and matrix metalloproteinase-2 (MMP2) expression. These data demonstrate that in certain biological contexts the non-enzymatic effects of HYAL2 are critical in orchestrating RhoA signaling and downstream pathways that are important for full pro-fibrotic myofibroblast functionality. In conjunction with previous data demonstrating the influence of HYAL2 on RNA splicing, these findings begin to explain the broad biological effects of HYAL2